satarupa22/MacromolecularLigandDB huggingface dataset:
MerTK kinase domain with type 3 inhibitor from a DNA-encoded library (PDB entry 7AW4)
Macromolecule: Tyrosine-protein kinase Mer
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 313 residues
Sequence: MGSSHHHHHHSSGLVPRGSEELQNKLEDVVIDRNLLILGKILGEGEFGSVMEGNLKQEDGTSLKVAVKTMKLDNSSQREIEEFLSEAACMKDFSHPNVIRLLGVCIEMSSQGIPKPMVILPFMKYGDLHTYLLYSRLETGPKHIPLQTLLKFMVDIALGMEYLSNRNFLHRDLAARNCMLRDDMTVCVADFGLSKKIYSGDYYRQGRIAKMPVKWIAIESLADRVYTSKSDVWAFGVTMWEIATRGMTPYPGVQNHEMYDYLLHGHRLKQPEDCLDELYEIMYSCWRTDPLDRPTFSVLRLQLEKLLESLPDV
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.98
R work: 0.214
R free: 0.246
Average B factor: 36.83
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.3 mM protein co-crystallised with 0.5 mM compound (1 % DMSO) in 25 % PEG3350, 0.2 M MgCl2, 0.1 M PCTP pH 7.5
Matthews coefficient: 2.18
Solvent content (%): 43.66
Ligand: 3-methyl-5-(4-methyl-1,2,3-thiadiazol-5-yl)-N-((R)-1-(((R)-3-(methylamino)-3-oxo-1-(4-(trifluoromethyl)phenyl)propyl)amino)-1-oxo-4-phenylbutan-2-yl)isoxazole-4-carboxamide (S5E)
Ligand formula: C29 H29 F3 N6 O4 S
Ligand molecular weight: 614.639
Ligand SMILES: Cc1c(c(on1)c2c(nns2)C)C(=O)NC(CCc3ccccc3)C(=O)NC(CC(=O)NC)c4ccc(cc4)C(F)(F)F
Ligand InChI: InChI=1S/C29H29F3N6O4S/c1-16-24(25(42-37-16)26-17(2)36-38-43-26)28(41)34-21(14-9-18-7-5-4-6-8-18)27(40)35-22(15-23(39)33-3)19-10-12-20(13-11-19)29(30,31)32/h4-8,10-13,21-22H,9,14-15H2,1-3H3,(H,33,39)(H,34,41)(H,35,40)/t21-,22-/m1/s1
Release date: 2021-03-03
CRYSTAL STRUCTURE OF BRUTON AGAMMAGLOBULINEMIA TYROSINE KINASE COMPLEXED WITH 4-[2-FLUORO-3-(4-OXO -3,4-DIHYDROQUINAZOLIN-3-YL)PHENYL]-7-(2-HYDROXYPROPAN-2-Y L)-9H-CARBAZOLE-1-CARBOXAMIDE (PDB entry 5JRS)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 267 residues
Sequence: GHMEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.97
R work: 0.202
R free: 0.226
Average B factor: 32.57
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8.5
Crystallization temperature (K): 298
Crystal growth procedure: PEG 5000, PEG 8000
Matthews coefficient: 2.27
Solvent content (%): 45.79
Ligand: 4-[2-fluoro-3-(4-oxoquinazolin-3(4H)-yl)phenyl]-7-(2-hydroxypropan-2-yl)-9H-carbazole-1-carboxamide (6MV)
Ligand formula: C30 H23 F N4 O3
Ligand molecular weight: 506.527
Ligand SMILES: CC(C)(c1ccc2c(c1)[nH]c3c2c(ccc3C(=O)N)c4cccc(c4F)N5C=Nc6ccccc6C5=O)O
Ligand InChI: InChI=1S/C30H23FN4O3/c1-30(2,38)16-10-11-19-23(14-16)34-27-21(28(32)36)13-12-17(25(19)27)18-7-5-9-24(26(18)31)35-15-33-22-8-4-3-6-20(22)29(35)37/h3-15,34,38H,1-2H3,(H2,32,36)
Release date: 2016-08-31
Crystal structure of human phosphodiesterase 2A with 1-(5-tert-butoxy-2-chloro-phenyl)-N-isobutyl-4-methyl-[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide (PDB entry 6C7J)
Macromolecule: cGMP-dependent 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.17
Sequence length: 342 residues
Sequence: SAMDDEYTKLLHDGIQPVAAIDSNFASFTYTPRSLPEDDTSMAILSMLQDMNFINNYKIDCPTLARFCLMVKKGYRDPPYHNWMHAFSVSHFCYLLYKNLELTNYLEDIEIFALFISCMCHDLDHRGTNNSFQVASKSVLAALYSSEGSVMERHHFAQAIAILNTHGCNIFDHFSRKDYQRMLDLMRDIILATDLAHHLRIFKDLQKMAEVGYDRNNKQHHRLLLCLLMTSCDLSDQTKGWKTTRKIAELIYKEFFSQGDLEKAMGNRPMEMMDREKAYIPELQISFMEHIAMPIYKLLQDLFPKAAELYERVASNREHWTKVSHKFTIRGLPSNNSLDFLD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1761
R free: 0.2302
Average B factor: 29.2075
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.4
Crystallization temperature (K): 293
Crystal growth procedure: 17-19% PEG3350, 0.2 M magnesium chloride, 0.1 M Tris, pH 8.4
Matthews coefficient: 2.21
Solvent content (%): 44.38
Ligand: 1-(5-tert-butoxy-2-chlorophenyl)-4-methyl-N-(2-methylpropyl)[1,2,4]triazolo[4,3-a]quinoxaline-8-carboxamide (EPV)
Ligand formula: C25 H28 Cl N5 O2
Ligand molecular weight: 465.975
Ligand SMILES: Cc1c2nnc(n2c3cc(ccc3n1)C(=O)NCC(C)C)c4cc(ccc4Cl)OC(C)(C)C
Ligand InChI: InChI=1S/C25H28ClN5O2/c1-14(2)13-27-24(32)16-7-10-20-21(11-16)31-22(15(3)28-20)29-30-23(31)18-12-17(8-9-19(18)26)33-25(4,5)6/h7-12,14H,13H2,1-6H3,(H,27,32)
Release date: 2018-08-15
Crystal structure of human DNA cross-link repair 1A in complex with N-hydroxyimide inhibitor H1 (PDB entry 8CEW)
Macromolecule: DNA cross-link repair 1A protein
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.2.6
Sequence length: 345 residues
Sequence: SMKKTCPFYKKIPGTGFTVDAFQYGVVEGCTAYFLTHFHSDHYAGLSKHFTFPVYCSEITGNLLKNKLHVQEQYIHPLPLDTECIVNGVKVVLLDANHCPGAVMILFYLPNGTVILHTGDFRADPSMERSLLADQKVHMLYLDTTYCSPEYTFPSQQEVIRFAINTAFEAVTLNPHALVVCGTYSIGKEKVFLAIADVLGSKVGMSQEKYKTLQCLNIPEINSLITTDMCSSLVHLLPMMQINFKGLQSHLKKCGGKYNQILAFRPTGWTHSNKFTRIADVIPQTKGNISIYGIPYSEHSSYLEMKRFVQWLKPQKIIPTVNVGTWKSRSTMEKYFREWKLEAGY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.53
R work: 0.1975
R free: 0.2236
Average B factor: 31.61
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 278
Crystal growth procedure: 30% PEG 1000, 0.1M MIB buffer
Matthews coefficient: 2.12
Solvent content (%): 42.02
Ligand: DIMETHYL SULFOXIDE (DMS)
Ligand formula: C2 H6 O S
Ligand molecular weight: 78.133
Ligand SMILES: CS(=O)C
Ligand InChI: InChI=1S/C2H6OS/c1-4(2)3/h1-2H3
Release date: 2024-02-21
Crystal structure of human NEIL1(P2G, E3Q, K242) bound to duplex DNA containing dihydrothymine (DHT) (PDB entry 6LWH)
Macromolecule: Endonuclease 8-like 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.2
Sequence length: 295 residues
Sequence: MGQGPELHLASQFVNEACRALVFGGCVEKSSVSRNPEVPFESSAYRISASARGKELRLILSPLPGAQPQQEPLALVFRFGMSGSFQLVPREELPRHAHLRFYTAPPGPRLALCFVDIRRFGRWDLGGKWQPGRGPCVLQEYQQFRENVLRNLADKAFDRPICEALLDQRFFNGIGNYLRAEILYRLKIPPFEKARSVLEALQQHRPSPELTLSQKIRTKLQNPDLLELCHSVPKEVVQLGGKGYGSESGEEDFAAFRAWLRCYGMPGMSSLQDRHGRTIWFQGDPGPLAPKGRKS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.78
R work: 0.2004
R free: 0.2422
Average B factor: 80.261
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277.15
Crystal growth procedure: 0.1 M cacodylic acid (pH 6.5), 0.1 M NaCl, 0.05 M MgCl2 and 18% (w/v) PEG 8000
Matthews coefficient: 2.73
Solvent content (%): 54.99
Ligand: GLYCEROL (GOL)
Ligand formula: C3 H8 O3
Ligand molecular weight: 92.094
Ligand SMILES: C(C(CO)O)O
Ligand InChI: InChI=1S/C3H8O3/c4-1-3(6)2-5/h3-6H,1-2H2
Release date: 2021-06-09
CCP5 apo structure (PDB entry 8V3M)
Macromolecule: Cytosolic carboxypeptidase-like protein 5
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.17
Sequence length: 524 residues
Sequence: NELRCGGLLFSSRFDSGNLAHVEKVESLSSDGEGVGGGASALTSGIASSPDYEFNVWTRPDCAETEFENGNRSWFYFSVRGGMPGKLIKINIMNMNKQSKLYSQGMAPFVRTLPTRPRWERIRDRPTFEMTETQFVLSFVHRFVEGRGATTFFAFCYPFSYSDCQELLNQLDQRFPENHPTHSSPLDTIYYHRELLCYSLDGLRVDLLTITSCHGLREDREPRLEQLFPDTSTPRPFRFAGKRIFFLSSRVHPGETPSSFVFNGFLDFILRPDDPRAQTLRRLFVFKLIPMLNPDGVVRGHYRTDSRGVNLNRQYLKPDAVLHPAIYGAKAVLLYHHVSGSGGSGVAYYVDLHGHASKRGCFMYGNSFSDESTQVENMLYPKLISLNSAHFDFQGCNFSEKNMYARDRRDGQSKEGSGRVAIYKASGIIHSYTLACNYNTGRSVNSIPAACHDNGRASPPPPPAFPSRYTVELFEQVGRAMAIAALDMAECNPWPRIVLSEHSSLTNLRAWMLKHVRNSRGLSS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1858
R free: 0.2009
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 294
Crystal growth procedure: 0.15 M DL-Malic acid, pH7.0, 0.1 M imidazole, pH7.0, 16% PEG MME 550
Matthews coefficient: 2.39
Solvent content (%): 48.48
Ligand: D-MALATE (MLT)
Ligand formula: C4 H6 O5
Ligand molecular weight: 134.087
Ligand SMILES: C(C(C(=O)O)O)C(=O)O
Ligand InChI: InChI=1S/C4H6O5/c5-2(4(8)9)1-3(6)7/h2,5H,1H2,(H,6,7)(H,8,9)/t2-/m1/s1
Release date: 2024-07-17
Structure of dead kinase MAPK14 with bound the KIM domain of MKK6 (PDB entry 5ETF)
Macromolecule: Mitogen-activated protein kinase 14
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.24
Sequence length: 360 residues
Sequence: MSQERPTFYRQELNKTIWEVPERYQNLSPVGSGAYGSVCAAFDTKTGLRVAVRKLSRPFQSIIHAKRTYRELRLLKHMKHENVIGLLDVFTPARSLEEFNDVYLVTHLMGADLNNIVKCQKLTDDHVQFLIYQILRGLKYIHSADIIHRDLKPSNLAVNEDCELKILDFGLARHTDDEMTGYVATRWYRAPEIMLNWMHYNQTVDIWSVGCIMAELLTGRTLFPGTDHIDQLKLILRLVGTPGAELLKKISSESARNYIQSLTQMPKMNFANVFIGANPLAVDLLEKMLVLDSDKRITAAQALAHAYFAQYHDPDDEPVADPYDQSFESRDLLIDEWKSLTYDEVISFVPPPLDQEEMES
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.4
R work: 0.1629
R free: 0.231
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 25% (w/v) PEG 3350 and 0.1 mM Bis-Tris pH6.5
Matthews coefficient: 2.81
Solvent content (%): 56.23
Release date: 2016-10-26
Crystal structure of LP_PLA2 in complex with novel inhibitor (PDB entry 5I8P)
Macromolecule: Platelet-activating factor acetylhydrolase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.47
Sequence length: 388 residues
Sequence: GPLGSAAASFGQTKIPRGNGPYSVGCTDLMFDHTNKGTFLRLYYPSQDNDRLDTLWIPNKEYFWGLSKFLGTHWLMGNILRLLFGSMTTPANWNSPLRPGEKYPLVVFSHGLGAFRTLYSAIGIDLASHGFIVAAVEHRDRSASATYYFKDQSAAEIGDKSWLYLRTLKQEEETHIRNEQVRQRAKECSQALSLILDIDHGKPVKNALDLKFDMEQLKDSIDREKIAVIGHSFGGATVIQTLSEDQRFRCGIALDAWMFPLGDEVYSRIPQPLFFINSEYFQYPANIIKMKKCYSPDKERKMITIRGSVHQNFADFTFATGKIIGHMLKLKGDIDSNVAIDLSNKASLAFLQKHLGLHKDFDQWDCLIEGDDENLIPGTNINTTNQHI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.37
R work: 0.2056
R free: 0.2745
Average B factor: 29.0238
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1M MOPS pH 6.6, 0.4M Li2SO4, 27% (w/v) (NH4)2SO4, 1M Na-Ac, 1.4% 1,4-butanediol
Matthews coefficient: 2.48
Solvent content (%): 50.43
Ligand: 6-[1,1-bis(oxidanylidene)-1,4-thiazinan-4-yl]-4-[[4-[4-chloranyl-3-(trifluoromethyl)phenoxy]-3,5-bis(fluoranyl)phenyl]methoxy]-1-methyl-pyrimidin-2-one (VQ7)
Ligand formula: C23 H19 Cl F5 N3 O5 S
Ligand molecular weight: 579.924
Ligand SMILES: CN1C(=CC(=NC1=O)OCc2cc(c(c(c2)F)Oc3ccc(c(c3)C(F)(F)F)Cl)F)N4CCS(=O)(=O)CC4
Ligand InChI: InChI=1S/C23H19ClF5N3O5S/c1-31-20(32-4-6-38(34,35)7-5-32)11-19(30-22(31)33)36-12-13-8-17(25)21(18(26)9-13)37-14-2-3-16(24)15(10-14)23(27,28)29/h2-3,8-11H,4-7,12H2,1H3
Release date: 2016-06-15
CDK2 with compound 14 inhibitor with carboxylate (PDB entry 7M2F)
Macromolecule: Cyclin-dependent kinase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 298 residues
Sequence: MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.632
R work: 0.2109
R free: 0.2575
Average B factor: 32.54
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.5
Crystallization temperature (K): 290
Crystal growth procedure: 20% PEG 10K, 0.1M HEPES
Matthews coefficient: 2
Solvent content (%): 38.4
Ligand: [(1r,4r)-4-{4-[4-(5-fluoro-2-methoxyphenyl)-1H-pyrrolo[2,3-b]pyridin-2-yl]-3,6-dihydropyridin-1(2H)-yl}cyclohexyl]acetic acid (YOS)
Ligand formula: C27 H30 F N3 O3
Ligand molecular weight: 463.544
Ligand SMILES: COc1ccc(cc1c2ccnc3c2cc([nH]3)C4=CCN(CC4)C5CCC(CC5)CC(=O)O)F
Ligand InChI: InChI=1S/C27H30FN3O3/c1-34-25-7-4-19(28)15-22(25)21-8-11-29-27-23(21)16-24(30-27)18-9-12-31(13-10-18)20-5-2-17(3-6-20)14-26(32)33/h4,7-9,11,15-17,20H,2-3,5-6,10,12-14H2,1H3,(H,29,30)(H,32,33)/t17-,20-
Release date: 2021-07-07
Structure of recombinant beta-glucocerebrosidase in complex with bifunctional cyclophellitol aziridine activity based probe (PDB entry 6Z3I)
Macromolecule: Lysosomal acid glucosylceramidase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.2.1.45
Sequence length: 497 residues
Sequence: ARPCIPKSFGYSSVVCVCNATYCDSFDPPTFPALGTFSRYESTRSGRRMELSMGPIQANHTGTGLLLTLQPEQKFQKVKGFGGAMTDAAALNILALSPPAQNLLLKSYFSEEGIGYNIIRVPMASCDFSIRTYTYADTPDDFQLHNFSLPEEDTKLKIPLIHRALQLAQRPVSLLASPWTSPTWLKTNGAVNGKGSLKGQPGDIYHQTWARYFVKFLDAYAEHKLQFWAVTAENEPSAGLLSGYPFQCLGFTPEHQRDFIARDLGPTLANSTHHNVRLLMLDDQRLLLPHWAKVVLTDPEAAKYVHGIAVHWYLDFLAPAKATLGETHRLFPNTMLFASEACVGSKFWEQSVRLGSWDRGMQYSHSIITNLLYHVVGWTDWNLALNPEGGPNWVRNFVDSPIIVDITKDTFYKQPMFYHLGHFSKFIPEGSQRVGLVASQKNDLDAVALMHPDGSAVVVVLNRSSKDVPLTIKDPAVGFLETISPGYSIHTYLWRRQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.8
R work: 0.1782
R free: 0.1894
Average B factor: 25.448
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Na2SO4, 0.25 M HEPES pH 7, PEG3350 14%, 1:1000 seed
Matthews coefficient: 2.43
Solvent content (%): 49.45
Ligand: SULFATE ION (SO4)
Ligand formula: O4 S
Ligand molecular weight: 96.063
Ligand SMILES: [O-]S(=O)(=O)[O-]
Ligand InChI: InChI=1S/H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/p-2
Release date: 2021-06-30
Identification of a New Zinc Binding Chemotype by Fragment Screening (PDB entry 5VGY)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHAFNVEFDDSQDKAVLKGGPLDGTYRLIQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDFGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTKGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLLECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.39
R work: 0.1129
R free: 0.15646
Average B factor: 15.279
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 281
Crystal growth procedure: concentrated CA II at 10 mg/mL was set up with microseeding over 2.9 M ammonium sulfate with 0.1 M Tris buffer at pH 8.3 at 8 C in 250 nL plus 225 nL plus 25 nL (seeds) ratio.
Matthews coefficient: 2.11
Solvent content (%): 41.64
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2017-08-30
Crystal structure of the TRS_UNE-T and 4EHP complex (PDB entry 5XLN)
Macromolecule: Threonine--tRNA ligase, cytoplasmic
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.1.1.3
Sequence length: 45 residues
Sequence: GGKKKNKEGSGDGGRAELNPWPEYIYTRLEMYNILKAEHDSILAE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.161
R free: 0.1964
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 9.5
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 8000,  0.1 M CHES (pH 9.5)
Matthews coefficient: 2.36
Solvent content (%): 47.78
Release date: 2018-11-21
DNA Polymerase Mu, dGTP:Ct Reaction State Ternary Complex, 10 mM Mn2+ (2min) (PDB entry 7KST)
Macromolecule: DNA-directed DNA/RNA polymerase mu
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 356 residues
Sequence: GSAAAPLSPAWMPAYACQRPTPLTHHNTGLSEALEILAEAAGFEGSEGRLLTFCRAASVLKALPSPVTTLSQLQGLPHFGEHSSRVVQELLEHGVCEEVERVRRSERYQTMKLFTQIFGVGVKTADRWYREGLRTLDDLREQPQKLTQQQKAGLQHHQDLSTPVLRSDVDALQQVVEEAVGQALPGATVTLTGGFRRGKLQGHDVDFLITHPKEGQEAGLLPRVMCRLQDQGLILYHQHQHSCCESPTRLAQQSHMDAFERSFCIFRLPQPGSWKAVRVDLVVAPVSQFPFALLGWTGSKLFQRELRRFSRKEKGLWLNSHGLFDPEQKTFFQAASEEDIFRHLGLEYLPPEQRNA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.599
R work: 0.1635
R free: 0.1852
Average B factor: 25.7713
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 85-90mM HEPES pH 7.5, 17-18% PEG4000
Matthews coefficient: 2.49
Solvent content (%): 50.66
Ligand: 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE (DGT)
Ligand formula: C10 H16 N5 O13 P3
Ligand molecular weight: 507.181
Ligand SMILES: c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H16N5O13P3/c11-10-13-8-7(9(17)14-10)12-3-15(8)6-1-4(16)5(26-6)2-25-30(21,22)28-31(23,24)27-29(18,19)20/h3-6,16H,1-2H2,(H,21,22)(H,23,24)(H2,18,19,20)(H3,11,13,14,17)/t4-,5+,6+/m0/s1
Release date: 2021-12-01
Vanin-1 complexed with Compound 11 (PDB entry 7SLX)
Macromolecule: Pantetheinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.5.1.92
Sequence length: 482 residues
Sequence: GSGHHHHHHGSGDYKDDDDKQDTFTAAVYEHAAILPNATLTPVSREEALALMNRNLDILEGAITSAADQGAHIIVTPEDAIYGWNFNRDSLYPYLEDIPDPEVNWIPCNNRNRFGQTPVQERLSCLAKNNSIYVVANIGDKKPCDTSDPQCPPDGRYQYNTDVVFDSQGKLVARYHKQNLFMGENQFNVPKEPEIVTFNTTFGSFGIFTCFDILFHDPAVTLVKDFHVDTIVFPTAWMNVLPHLSAVEFHSAWAMGMRVNFLASNIHYPSKKMTGSGIYAPNSSRAFHYDMKTEEGKLLLSQLDSHPSHSAVVNWTSYASSIEALSSGNKEFKGTVFFDEFTFVKLTGVAGNYTVCQKDLCCHLSYKMSENIPNEVYALGAFDGLHTVEGRYYLQICTLLKCKTTNLNTCGDSAETASTRFEMFSLSGTFGTQYVFPEVLLSENQLAPGEFQVSTDGRLFSLKPTSGPVLTVTLFGRLYEKD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1739
R free: 0.2172
Average B factor: 59.19
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 100 mM MES pH 6.1-6.7, 22-33% PEG-MME-2000, 10 mM TCEP
Matthews coefficient: 2.47
Solvent content (%): 50.27
Ligand: 2-acetamido-2-deoxy-beta-D-glucopyranose (NAG)
Ligand formula: C8 H15 N O6
Ligand molecular weight: 221.208
Ligand SMILES: CC(=O)NC1C(C(C(OC1O)CO)O)O
Ligand InChI: InChI=1S/C8H15NO6/c1-3(11)9-5-7(13)6(12)4(2-10)15-8(5)14/h4-8,10,12-14H,2H2,1H3,(H,9,11)/t4-,5-,6-,7-,8-/m1/s1
Release date: 2022-01-12
Human E105Qa GTP-specific succinyl-CoA synthetase complexed with succinyl-phosphate, magnesium ion and desulfo-coenzyme A (PDB entry 7MSR)
Macromolecule: Succinate--CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.2.1.4
Sequence length: 315 residues
Sequence: MSYTASRQHLYVDKNTKIICQGFTGKQGTFHSQQALEYGTKLVGGTTPGKGGQTHLGLPVFNTVKEAKEQTGATASVIYVPPPFAAAAINEAIEAEIPLVVCITQGIPQQDMVRVKHKLLRQEKTRLIGPNCPGVINPGECKIGIMPGHIHKKGRIGIVSRSGTLTYEAVHQTTQVGLGQSLCVGIGGDPFNGTDFIDCLEIFLNDSATEGIILIGEIGGNAEENAAEFLKQHNSGPNSKPVVSFIAGLTAPPGRRMGHAGAIIAGGKGGAKEKISALQSAGVVVSMSPAQLGTTIYKEFEKRKMLEHHHHHHHH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.58
R work: 0.1987
R free: 0.2213
Average B factor: 40.8869
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 22.5% (w/v) PEG3350, 100 mM ammonium succinate pH 7.5, 100 mM Tris-HCl pH 7.4
Matthews coefficient: 2.27
Solvent content (%): 45.9
Ligand: DESULFO-COENZYME A (DCA)
Ligand formula: C21 H36 N7 O16 P3
Ligand molecular weight: 735.469
Ligand SMILES: CCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)OP(=O)(O)O)O
Ligand InChI: InChI=1S/C21H36N7O16P3/c1-4-23-12(29)5-6-24-19(32)16(31)21(2,3)8-41-47(38,39)44-46(36,37)40-7-11-15(43-45(33,34)35)14(30)20(42-11)28-10-27-13-17(22)25-9-26-18(13)28/h9-11,14-16,20,30-31H,4-8H2,1-3H3,(H,23,29)(H,24,32)(H,36,37)(H,38,39)(H2,22,25,26)(H2,33,34,35)/t11-,14-,15-,16+,20-/m1/s1
Release date: 2022-10-12
Crystal structure of MavC ternary complex (PDB entry 6KFP)
Macromolecule: MavC
Type: Protein, polypeptide(L)
Source organism: Legionella pneumophila
Sequence length: 378 residues
Sequence: EKTGLHVHEKIKHMVKNYGTMITGIPAEILGQNEAEISVGYVKKMGNMKENIAEVVRKSEMTQPTNSAGKASNEVCDLLLGTEGASEFEKSSYQVLSGDGSNLKGSLPNKNLLVRVEMDRFNAPQKYQKIKREEFNPETAEKNKIYLLEDQLVYLDIFGKVIDLGQTSDTCHRLFNAITTPFYQNYILYDEYIDPEESAEEAAMFEMGEIVKAKMKNIDCWTATHSFTIFVPESDSEDTRTLYPYQAYWTSHTLQQWFSGDKDEKLSRLGIDGYIEKLALLGTTTDSKIRSSIYGELFSPPGKEHVFCTGMNEKFSPLRVKFKVTEVNPEIALQNLEEVQEFIDTNYPGENAKDQCELYKIKAQEAMTKQLEMRLLIE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.92
R work: 0.1932
R free: 0.2498
Average B factor: 53.62
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: PEG 3350, lithium chloride
Matthews coefficient: 2.39
Solvent content (%): 48.63
Release date: 2020-04-01
Human NOQ1 enzyme in complex with NADH by serial crystallography (PDB entry 8RFM)
Macromolecule: NAD(P)H dehydrogenase [quinone] 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.6.5.2
Sequence length: 274 residues
Sequence: MVGRRALIVLAHSERTSFNYAMKEAAAAALKKKGWEVVESDLYAMNFNPIISRKDITGKLKDPANFQYPAESVLAYKEGHLSPDIVAEQKKLEAADLVIFQFPLQWFGVPAILKGWFERVFIGEFAYTYAAMYDKGPFRSKKAVLSITTGGSGSMYSLQGIHGDMNVILWPIQSGILHFCGFQVLEPQLTYSIGHTPADARIQILEGWKKRLENIWDETPLYFAPSSLFDLNFQAGFLMKKEVQDEEKNKKFGLSVGHHLGKSIPTDNQIKARK
Oligomeric state: Homo 4-mer
Stoichiometry: A4
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.7
R work: 0.19848
R free: 0.24254
Average B factor: 65.395
Crystallization method: BATCH MODE
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M Tris pH 8.5, 0.2 M sodium acetate, 20% polyethylene glycol (PEG) 3350
Matthews coefficient: 2.58
Solvent content (%): 52.41
Ligand: NICOTINAMIDE-ADENINE-DINUCLEOTIDE (NAD)
Ligand formula: C21 H27 N7 O14 P2
Ligand molecular weight: 663.425
Ligand SMILES: c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
Ligand InChI: InChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
Release date: 2024-05-29
Crystal structure of HCK complexed with a pyrrolo-pyrimidine inhibitor (S)-2-(((1r,4S)-4-(4-amino-5-(4-phenoxyphenyl)-7H-pyrrolo[2,3-d]pyrimidin-7-yl)cyclohexyl)amino)-N,N,4-trimethylpentanamide (PDB entry 5H0H)
Macromolecule: Tyrosine-protein kinase HCK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 454 residues
Sequence: GAMGSGIRIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEEWFFKGISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDYDPRQGDTVKHYKIRTLDNGGFYISPRSTFSTLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDAWEIPRESLKLEKKLGAGQFGEVWMATYNKHTKVAVKTMKPGSMSVEAFLAEANVMKTLQHDKLVKLHAVVTKEPIYIITEFMAKGSLLDFLKSDEGSKQPLPKLIDFSAQIAEGMAFIEQRNYIHRDLRAANILVSASLVCKIADFGLARVIEDNEYTAREGAKFPIKWTAPEAINFGSFTIKSDVWSFGILLMEIVTYGRIPYPGMSNPEVIRALERGYRMPRPENCPEELYNIMMRCWKNRPEERPTFEYIQSVLDDFYTATESQYEEIP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.72
R work: 0.185
R free: 0.2239
Average B factor: 37.3881
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.22-0.25 M ammonium formate, 12-22 % PEG 3350
Matthews coefficient: 2.32
Solvent content (%): 46.87
Ligand: (2~{S})-2-[[4-[4-azanyl-5-(4-phenoxyphenyl)pyrrolo[2,3-d]pyrimidin-7-yl]cyclohexyl]amino]-~{N},~{N},4-trimethyl-pentanamide (OOV)
Ligand formula: C32 H40 N6 O2
Ligand molecular weight: 540.699
Ligand SMILES: CC(C)CC(C(=O)N(C)C)NC1CCC(CC1)n2cc(c3c2ncnc3N)c4ccc(cc4)Oc5ccccc5
Ligand InChI: InChI=1S/C32H40N6O2/c1-21(2)18-28(32(39)37(3)4)36-23-12-14-24(15-13-23)38-19-27(29-30(33)34-20-35-31(29)38)22-10-16-26(17-11-22)40-25-8-6-5-7-9-25/h5-11,16-17,19-21,23-24,28,36H,12-15,18H2,1-4H3,(H2,33,34,35)/t23-,24-,28-/m0/s1
Release date: 2017-10-04