satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of MUS81-EME1 bound by compound 12. (PDB entry 9F9A)
Macromolecule: Crossover junction endonuclease MUS81
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.22
Sequence length: 308 residues
Sequence: GSSAELASEAGVQQQPLELRPGEYRVLLCVDIGETRGGGHRPELLRELQRLHVTHTVRKLHVGDFVWVAQETNPRDPANPGELVLDHIVERKRLDDLCSSIIDGRFREQKFRLKRCGLERRVYLVEEHGSVHNLSLPESTLLQAVTNTQVIDGFFVKRTADIKESAAYLALLTRGLQRLYQGHTLRSRPWGTPGNPESGAMTSPNPLCSLLTFSDFNAGAIKNKAQSVREVFARQLMQVRGVSGEKAAALVDRYSTPASLLAAYDACATPKEQETLLSTIKCGRLQRNLGPALSRTLSQLYCSYGPLT
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.911
R work: 0.2429
R free: 0.2782
Average B factor: 70
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 297
Crystal growth procedure: 20 % ethanol
Matthews coefficient: 2.69
Solvent content (%): 54.29
Ligand: 2-naphthalen-2-yl-5-oxidanyl-6-oxidanylidene-1H-pyrimidine-4-carboxylic acid (A1IA6)
Ligand formula: C15 H10 N2 O4
Ligand molecular weight: 282.251
Ligand SMILES: c1ccc2cc(ccc2c1)C3=NC(=C(C(=O)N3)O)C(=O)O
Ligand InChI: InChI=1S/C15H10N2O4/c18-12-11(15(20)21)16-13(17-14(12)19)10-6-5-8-3-1-2-4-9(8)7-10/h1-7,18H,(H,20,21)(H,16,17,19)
Release date: 2024-06-19
Human PPARgamma ligand binding domain complexed with Rosiglitazone (PDB entry 5YCP)
Macromolecule: Peroxisome proliferator-activated receptor gamma
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 283 residues
Sequence: AEISSDIDQLNPESADLRALAKHLYDSYIKSFPLTKAKARAILTGKTTDKSPFVIYDMNSLMMGEDKIKFKHITPLQEQSKEVAIRIFQGCQFRSVEAVQEITEYAKSIPGFVNLDLNDQVTLLKYGVHEIIYTMLASLMNKDGVLISEGQGFMTREFLKSLRKPFGDFMEPKFEFAVKFNALELDDSDLAIFIAVIILSGDRPGLLNVKPIEDIQDNLLQALELQLKLNHPESSQLFAKLLQKMTDLRQIVTEHVQLLQVIKKTETDMSLHPLLQEIYKDLY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.0
R work: 0.20132
R free: 0.23338
Average B factor: 44.458
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 296
Crystal growth procedure: 2.2 M sodium malonate (pH 7.0)
Matthews coefficient: 2.77
Solvent content (%): 55.65
Ligand: 2,4-THIAZOLIDIINEDIONE, 5-[[4-[2-(METHYL-2-PYRIDINYLAMINO)ETHOXY]PHENYL]METHYL]-(9CL) (BRL)
Ligand formula: C18 H19 N3 O3 S
Ligand molecular weight: 357.427
Ligand SMILES: CN(CCOc1ccc(cc1)CC2C(=O)NC(=O)S2)c3ccccn3
Ligand InChI: InChI=1S/C18H19N3O3S/c1-21(16-4-2-3-9-19-16)10-11-24-14-7-5-13(6-8-14)12-15-17(22)20-18(23)25-15/h2-9,15H,10-12H2,1H3,(H,20,22,23)/t15-/m0/s1
Release date: 2018-09-12
Carborane nido-pentyl-sulfonamide in complex with CA IX mimic (PDB entry 6YZM)
Macromolecule: Carbonic anhydrase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 4.2.1.1
Sequence length: 260 residues
Sequence: MSHHWGYGKHNGPEHWHKDFPIAKGERQSPVDIDTHTAKYDPSLKPLSVSYDQATSLRILNNGHSFQVTFDDSQDKAVLKGGPLDGTYRLLQFHFHWGSLDGQGSEHTVDKKKYAAELHLVHWNTKYGDVGKAVQQPDGLAVLGIFLKVGSAKPGLQKVVDVLDSIKTEGKSADFTNFDPRGLLPESLDYWTYPGSLTTPPLAECVTWIVLKEPISVSSEQVLKFRKLNFNGEGEPEELMVDNWRPAQPLKNRQIKASFK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.5
R work: 0.1629
R free: 0.1945
Average B factor: 21.415
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.8
Crystallization temperature (K): 291
Crystal growth procedure: 1.6 M sodium citrate, 50 mM Tris-H2SO4
Matthews coefficient: 2.02
Solvent content (%): 39.24
Ligand: Carborane nido-pentyl-sulfonamide (Q4B)
Ligand formula: C7 H12 B9 N O2 S
Ligand molecular weight: 271.54
Ligand SMILES: B123B45B167B289B31B823B966B744B622C45C321CCCCCS(=O)(=O)N
Ligand InChI: InChI=1S/C7H12B9NO2S/c17-20(18,19)5-3-1-2-4-7-6-8-10-9(7)13(7)11(6,7)12(6,8)14(8,10)15(9,10,13)16(11,12,13)14/h1-5H2,(H2,17,18,19)
Release date: 2020-10-28
Structure of PPIA in complex with FP29102, a Helicon Polypeptide (PDB entry 7UXJ)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 166 residues
Sequence: GMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.07
R work: 0.2244
R free: 0.2616
Average B factor: 40.5793
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291.15
Crystal growth procedure: 0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
Matthews coefficient: 2.18
Solvent content (%): 43.54
Ligand: AMINO GROUP (NH2)
Ligand formula: H2 N
Ligand molecular weight: 16.023
Ligand SMILES: [NH2]
Ligand InChI: InChI=1S/H3N/h1H3
Release date: 2022-12-28
DDR1, 3-[(3-cyclopropyl-1,2,4-oxadiazol-5-yl)methyl]-8-(1H-indazole-5-carbonyl)-1-phenyl-1,3,8-triazaspiro[4.5]decan-4-one, 1.670A, P1211, Rfree=22.8% (PDB entry 6FIN)
Macromolecule: Epithelial discoidin domain-containing receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 321 residues
Sequence: PGAVGDGPPRVDFPRSRLRFKEKLGEGQFGEVHLCEVDSPQDLVSLDFPLNVRKGHPLLVAVKILRPDATKNARNDFLKEVKIMSRLKDPNIIRLLGVCVQDDPLCMITDYMENGDLNQFLSAHQLEDKAAEGAPGDPTISYPMLLHVAAQIASGMRYLATLNFVHRDLATRNCLVGENFTIKIADFGMSRNLYAGDYYRVQGRAVLPIRWMAWECILMGKFTTASDVWAFGVTLWEVLMLCRAQPFGQLTDEQVIENAGEFFRDQGRQVYLSRPPACPQGLYELMLRCWSRESEQRPPFSQLHRFLAEDALNTVHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.67
R work: 0.198
R free: 0.2279
Average B factor: 37.1356
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.5
Crystallization temperature (K): 293
Crystal growth procedure: 11.3 mg/mL protein in 20mM HEPES/NaOH pH7.5, 5mM DTT, 5% glycerol, 0.1M NaCl mixed 1.3:1 with 90mM MES/NaOH pH6.5, 0.18M potassium iodide, 0.2M Li2SO4, 22.5% PEG 4K
Matthews coefficient: 2.14
Solvent content (%): 42.41
Ligand: 3-[(3-cyclopropyl-1,2,4-oxadiazol-5-yl)methyl]-8-(1~{H}-indazol-5-ylcarbonyl)-1-phenyl-1,3,8-triazaspiro[4.5]decan-4-one (DJQ)
Ligand formula: C27 H27 N7 O3
Ligand molecular weight: 497.548
Ligand SMILES: c1ccc(cc1)N2CN(C(=O)C23CCN(CC3)C(=O)c4ccc5c(c4)cn[nH]5)Cc6nc(no6)C7CC7
Ligand InChI: InChI=1S/C27H27N7O3/c35-25(19-8-9-22-20(14-19)15-28-30-22)32-12-10-27(11-13-32)26(36)33(17-34(27)21-4-2-1-3-5-21)16-23-29-24(31-37-23)18-6-7-18/h1-5,8-9,14-15,18H,6-7,10-13,16-17H2,(H,28,30)
Release date: 2018-11-28
SRPK1 IN COMPLEX WITH INHIBITOR (PDB entry 7ZKS)
Macromolecule: SRSF protein kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 387 residues
Sequence: GSDDDEQEDPNDYCKGGYHLVKIGDLFNGRYHVIRKLGWGHFSTVWLSWDIQGKKFVAMKVVKSAEHYTETALDEIRLLKSVRNSDPNDPNREMVVQLLDDFKISGVNGTHICMVFEVLGHHLLKWIIKSNYQGLPLPCVKKIIQQVLQGLDYLHTKCRIIHTDIKPENILLSVNEQYIRRLAAEATEWQRSGAPPPSGSAVSTAPAGNFLVNPLEPKNAEKLKVKIADLGNACWVHKHFTEDIQTRQYRSLEVLIGSGYNTPADIWSTACMAFELATGDYLFEPHSGEEYTRDEDHIALIIELLGKVPRKLIVAGKYSKEFFTKKGDLKHITKLKPWGLFEVLVEKYEWSQEEAAGFTDFLLPMLELIPEKRATAAECLRHPWLNS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.2428
R free: 0.2897
Average B factor: 52.35
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 5 mM HEPES pH 7.4, 150 mM NaCl, 20 mM DTT
Matthews coefficient: 3.01
Solvent content (%): 59.1
Ligand: N-[3-[[[2-(6-chloranyl-5-fluoranyl-1H-benzimidazol-2-yl)pyrimidin-4-yl]amino]methyl]pyridin-2-yl]-N-methyl-methanesulfonamide (IXQ)
Ligand formula: C19 H17 Cl F N7 O2 S
Ligand molecular weight: 461.9
Ligand SMILES: CN(c1c(cccn1)CNc2ccnc(n2)c3[nH]c4cc(c(cc4n3)F)Cl)S(=O)(=O)C
Ligand InChI: InChI=1S/C19H17ClFN7O2S/c1-28(31(2,29)30)19-11(4-3-6-23-19)10-24-16-5-7-22-17(27-16)18-25-14-8-12(20)13(21)9-15(14)26-18/h3-9H,10H2,1-2H3,(H,25,26)(H,22,24,27)
Release date: 2023-02-22
Crystal structure of human NRMT1 in complex with alpha-N-dimethylated human CENP-A peptide (PDB entry 5CVD)
Macromolecule: N-terminal Xaa-Pro-Lys N-methyltransferase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.244
Sequence length: 243 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMTSEVIEDEKQFYSKAKTYWKQIPPTVDGMLGGYGHISSIDINSSRKFLQRFLREGPNKTGTSCALDCGAGIGRITKRLLLPLFREVDMVDITEDFLVQAKTYLGEEGKRVRNYFCCGLQDFTPEPDSYDVIWIQWVIGHLTDQHLAEFLRRCKGSLRPNGIIVIKDNMAQEGVILDDVDSSVCRDLDVVRRIICSAGLSLLAEERQENLPDEIYHVYSFALR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1322
R free: 0.16
Average B factor: 14.1414
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5.6
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M (NH4)Ac, 0.1 M Sodium citrate tribasic dihydrate, 28%(w/v) PEG 4000
Matthews coefficient: 2.17
Solvent content (%): 43.21
Ligand: S-ADENOSYL-L-HOMOCYSTEINE (SAH)
Ligand formula: C14 H20 N6 O5 S
Ligand molecular weight: 384.411
Ligand SMILES: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
Ligand InChI: InChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
Release date: 2015-11-25
HUMAN ARTD2 (PARP2) - CATALYTIC DOMAIN IN COMPLEX WITH OLAPARIB (PDB entry 4TVJ)
Macromolecule: Poly [ADP-ribose] polymerase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 368 residues
Sequence: MHHHHHHSSGVDLGTENLYFQSMDLRVQELIKLICNVQAMEEMMMEMKYNTKKAPLGKLTVAQIKAGYQSLKKIEDCIRAGQHGRALMEACNEFYTRIPHDFGLRTPPLIRTQKELSEKIQLLEALGDIEIAIKLVKTELQSPEHPLDQHYRNLHCALRPLDHESYEFKVISQYLQSTHAPTHSDYTMTLLDLFEVEKDGEKEAFREDLHNRMLLWHGSRMSNWVGILSHGLRIAHPEAPITGYMFGKGIYFADMSSKSANYCFASRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTVPLGPASDTGILNPDGYTLNYNEYIVYNPNQVRMRYLLKVQFNF
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.1
R work: 0.18763
R free: 0.23103
Average B factor: 27.879
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 25% PEG3350, 0.1M Tris
Matthews coefficient: 2.4
Solvent content (%): 48.74
Ligand: 4-(3-{[4-(cyclopropylcarbonyl)piperazin-1-yl]carbonyl}-4-fluorobenzyl)phthalazin-1(2H)-one (09L)
Ligand formula: C24 H23 F N4 O3
Ligand molecular weight: 434.463
Ligand SMILES: c1ccc2c(c1)C(=NNC2=O)Cc3ccc(c(c3)C(=O)N4CCN(CC4)C(=O)C5CC5)F
Ligand InChI: InChI=1S/C24H23FN4O3/c25-20-8-5-15(14-21-17-3-1-2-4-18(17)22(30)27-26-21)13-19(20)24(32)29-11-9-28(10-12-29)23(31)16-6-7-16/h1-5,8,13,16H,6-7,9-12,14H2,(H,27,30)
Release date: 2015-07-08
Structure of human plasma factor XIIa in complex with (2S)-1-(N,3-dicyclohexyl-D-alanyl)-4-[(4R,5S)-4-methyl-5-phenyl-4,5-dihydro-1,3-oxazol-2-yl]-N-[(thiophen-2-yl)methyl]piperazine-2-carboxamide (compound 8h) (PDB entry 6X0T)
Macromolecule: Coagulation factor XII
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.21.38
Sequence length: 259 residues
Sequence: LSCGQRLRKSLSSMTRVVGGLVALRGAHPYIAALYWGHSFCAGSLIAPCWVLTAAHCLQDRPAPEDLTVVLGQERRNHSCEPCQTLAVRSYRLHEAFSPVSYQHDLALLRLQEDADGSCALLSPYVQPVCLPSGAARPSETTLCQVAGWGHQFEGAEEYASFLQEAQVPFLSLERCSAPDVHGSSILPGMLCAGFLEGGTDACQGDSGGPLVCEDQAAERRLTLQGIISWGSGCGDRNKPGVYTDVAYYLAWIREHTVS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.388
R work: 0.2889
R free: 0.3112
Average B factor: 10.82
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.3
Crystallization temperature (K): 291
Crystal growth procedure: 18% PEG3350, 200 mM lithium sulfate, 0.7 mM cadmium chloride, 100 mM Bis-Tris, pH 6.3
Matthews coefficient: 2.64
Solvent content (%): 53.44
Ligand: (2S)-1-(N,3-dicyclohexyl-D-alanyl)-4-[(4R,5S)-4-methyl-5-phenyl-4,5-dihydro-1,3-oxazol-2-yl]-N-[(thiophen-2-yl)methyl]piperazine-2-carboxamide (UJ7)
Ligand formula: C35 H49 N5 O3 S
Ligand molecular weight: 619.86
Ligand SMILES: CC1C(OC(=N1)N2CCN(C(C2)C(=O)NCc3cccs3)C(=O)C(CC4CCCCC4)NC5CCCCC5)c6ccccc6
Ligand InChI: InChI=1S/C35H49N5O3S/c1-25-32(27-14-7-3-8-15-27)43-35(37-25)39-19-20-40(31(24-39)33(41)36-23-29-18-11-21-44-29)34(42)30(22-26-12-5-2-6-13-26)38-28-16-9-4-10-17-28/h3,7-8,11,14-15,18,21,25-26,28,30-32,38H,2,4-6,9-10,12-13,16-17,19-20,22-24H2,1H3,(H,36,41)/t25-,30-,31+,32-/m1/s1
Release date: 2021-05-19
Crystal structure of GDP bound RhoA protein (PDB entry 6KX2)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 181 residues
Sequence: MAAIRKKLVIVGDGAVGKTSLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMVFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMETSAKTKDGVREVFEMATRAALQA
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.454
R work: 0.1842
R free: 0.2104
Average B factor: 22.978
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 4.5
Crystallization temperature (K): 289
Crystal growth procedure: 10 mg/mL mutant, 0.2M NaCl; 0.1M acetate Na (pH 4.5) and 1.26M ammonium sulfate
Matthews coefficient: 2.93
Solvent content (%): 58.04
Ligand: GUANOSINE-5'-DIPHOSPHATE (GDP)
Ligand formula: C10 H15 N5 O11 P2
Ligand molecular weight: 443.201
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H15N5O11P2/c11-10-13-7-4(8(18)14-10)12-2-15(7)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,22,23)(H2,19,20,21)(H3,11,13,14,18)/t3-,5-,6-,9-/m1/s1
Release date: 2020-08-19
Cryogenic Human Hsp90a-NTD bound to N6M (PDB entry 7S98)
Macromolecule: Heat shock protein HSP 90-alpha
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.4.10
Sequence length: 237 residues
Sequence: HMPEETQTQDQPMEEEEVETFAFQAEIAQLMSLIINTFYSNKEIFLRELISNSSDALDKIRYESLTDPSKLDSGKELHINLIPNKQDRTLTIVDTGIGMTKADLINNLGTIAKSGTKAFMEALQAGADISMIGQFGVGFYSAYLVAEKVTVITKHNDDEQYAWESSAGGSFTVRTDTGEPMGRGTKVILHLKEDQTEYLEERRIKEIVKKHSQFIGYPITLFVEKERDKEVSDDEAE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.186
R free: 0.2162
Average B factor: 40.09
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 1.8 M Malic acid, pH 7
Matthews coefficient: 2.81
Solvent content (%): 56.25
Ligand: N-METHYL-9H-PURIN-6-AMINE (N6M)
Ligand formula: C6 H7 N5
Ligand molecular weight: 149.153
Ligand SMILES: CNc1c2c([nH]cn2)ncn1
Ligand InChI: InChI=1S/C6H7N5/c1-7-5-4-6(10-2-8-4)11-3-9-5/h2-3H,1H3,(H2,7,8,9,10,11)
Release date: 2022-08-03
Crystal structure of IDO1 in complex with Apoxidole-1 (PDB entry 8ABX)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 404 residues
Sequence: GPLGSGIQMENSWTISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.65
R work: 0.192
R free: 0.21
Average B factor: 33.6008
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 40% PEG200, 100mM MES
Matthews coefficient: 2.33
Solvent content (%): 47.27
Ligand: TETRAETHYLENE GLYCOL (PG4)
Ligand formula: C8 H18 O5
Ligand molecular weight: 194.226
Ligand SMILES: C(COCCOCCOCCO)O
Ligand InChI: InChI=1S/C8H18O5/c9-1-3-11-5-7-13-8-6-12-4-2-10/h9-10H,1-8H2
Release date: 2022-08-24
Carbonic anhydrase 2 with inhibitor (2Z)-2-[(4-methoxyphenyl)methylidene]-3-oxo-N-(4-sulfamoylphenyl)butanamide (11d/D4) (PDB entry 6UFC)
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): 1.325
R work: 0.1168
R free: 0.1443
Average B factor: 14.341
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 281
Crystal growth procedure: 200 nL 7 mg/mL protein + 200 nL reservoir solution (2.5-2.8 M ammonium sulfate, 100 mM Tris, pH 8.5-9.0)
Matthews coefficient: 2.11
Solvent content (%): 41.78
Ligand: ZINC ION (ZN)
Ligand formula: Zn
Ligand molecular weight: 65.409
Ligand SMILES: [Zn+2]
Ligand InChI: InChI=1S/Zn/q+2
Release date: 2020-08-05
Crystal Structure of HD-PTP phosphatase in complex with UBAP1 (PDB entry 5LM1)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 23
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 352 residues
Sequence: PMAAHEASSLYSEEKAKLLREMMAKIEDKNEVLDQFMDSMQLDPETVDNLDAYSHIPPQLMEKCAALSVRPDTVRNLVQSMQVLSGVFTDVEASLKDIRDLLEEDELLEQKFQEAVGQAGAISITSKAELAEVRREWAKYMEVHEKASFTNSELHRAMNLHVGNLRLLSGPLDQVRAALPTPALSPEDKAVLQNLKRILAKVQEMRDQRVSLEQQLRELIQKDDITASLVTTDHSEMKKLFEEQLKKYDQLKVYLEQNLAAQDRVLCALTEANVQYAAVRRVLSDLDQKWNSTLQTLVASYEAYEDLMKKSQEGRDFYADLESKVAALLERTQSTCQAREAARQQLLDRELK
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.55
R work: 0.213
R free: 0.2539
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 294
Crystal growth procedure: 0.2 M KSCN, 20% PEG3350
Matthews coefficient: 2.65
Solvent content (%): 53.53
Release date: 2016-11-30
Diphosphoinositol polyphosphate phosphohydrolase 1 (DIPP1/NUDT3) in complex with inositol hexakisphosphate and Mg, presoaked with 5-IP7, Mg and Fluoride, soaking 20min in the absence of Fluoride. (PDB entry 6WOF)
Macromolecule: Diphosphoinositol polyphosphate phosphohydrolase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.1.52
Sequence length: 169 residues
Sequence: HHHHHHSSGVDLGTENLYFQSMMKLKSNQTRTYDGDGYKKRAACLCFRSESEEEVLLVSSSRHPDRWIVPGGGMEPEEEPSVAAVREVCEEAGVKGTLGRLVGIFENQERKHRTYVYVLIVTEVLEDWEDSVNIGRKREWFKIEDAIKVLQYHKPVQASYFETLRQGYS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.6
R work: 0.1227
R free: 0.1484
Average B factor: 16.326
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 10% (w/v) PEG 8000, 10% (v/v) isopropanol, 200 mM Li2SO4, 75 mM NaAc, pH 5.5 and 25 mM HEPES, pH 7.0 and soaking in solution of 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 80 mM NaF, 20 mM MgCl2 in present of 2mM 5-IP7 for 2 days, and transferred into 200 mM LiCl, 20% (w/v) PEG 8000, 20% (v/v) isopropanol, 100 mM HEPES, pH 7.0, 20 mM MgCl2 for 20 min.
Matthews coefficient: 2.21
Solvent content (%): 44.38
Ligand: MAGNESIUM ION (MG)
Ligand formula: Mg
Ligand molecular weight: 24.305
Ligand SMILES: [Mg+2]
Ligand InChI: InChI=1S/Mg/q+2
Release date: 2021-03-03
CRYSTAL STRUCTURE OF MONOBODY AS25/ABL1 SH2 DOMAIN COMPLEX, CRYSTAL B (PDB entry 5DC9)
Macromolecule: Tyrosine-protein kinase ABL1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 123 residues
Sequence: GSPSNYITPVNSLEKHSWYHGPVSRNAAEYLLSSGINGSFLVRESESSPGQRSISLRYEGRVYHYRINTASDGKLYVSSESRFNTLAELVHHHSTVADGLITTLHYPAPKRNKPTVYGVSPNY
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.56
R work: 0.13652
R free: 0.1706
Average B factor: 18.977
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 292
Crystal growth procedure: 0.1M Imidazole pH 8.5 and 3.4M NaCl
Matthews coefficient: 2.91
Solvent content (%): 57.71
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: 2016-03-02
Ancestral Caspase 6 (PDB entry 6PPM)
Macromolecule: Ancestral Caspase-6 Large Subunit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.22.59
Sequence length: 151 residues
Sequence: FYKREMFDPAEEYKMNHKRRGLALIFNQKRFDWKLGLKTRNGTDKDRDNLERRFQELGFEVKAYNDLSAEEVLEKIQEASTADHSDADCFVCVFLSHGEDGHVYANDAKIEIQELTNLFKGDKCQSLVGKPKIFIIQACRGDKLDDAVTPM
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.61
R work: 0.1775
R free: 0.2509
Average B factor: 54.5
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.2 M ammonium fluoride, pH 6.2, 20% PEG 3350
Matthews coefficient: 2.35
Solvent content (%): 47.6
Release date: 2019-11-13
Fragment-Based Discovery of a Novel Bruton's Tyrosine Kinase Inhibitor (PDB entry 7N5R)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 283 residues
Sequence: GPLPGKNAPSTAGLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.55
R work: 0.1713
R free: 0.195
Average B factor: 16.769
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 277
Crystal growth procedure: 10% polyethylene glycol 4000, 20% glycerol, 0.1M imidazole/MES, pH 6.5 and 0.12M alcohol mixture
Matthews coefficient: 2.21
Solvent content (%): 44.36
Ligand: IMIDAZOLE (IMD)
Ligand formula: C3 H5 N2
Ligand molecular weight: 69.085
Ligand SMILES: c1c[nH+]c[nH]1
Ligand InChI: InChI=1S/C3H4N2/c1-2-5-3-4-1/h1-3H,(H,4,5)/p+1
Release date: 2021-09-08
Tricomplex of RMC-7977, KRAS G12S, and CypA (PDB entry 8TBN)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 166 residues
Sequence: SMVNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.1529
R free: 0.1966
Average B factor: 30.79
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 291
Crystal growth procedure: 22% PEG6000, 0.1 M imidazole, pH 7
Matthews coefficient: 2.36
Solvent content (%): 47.78
Ligand: PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER (GNP)
Ligand formula: C10 H17 N6 O13 P3
Ligand molecular weight: 522.196
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C10H17N6O13P3/c11-10-13-7-4(8(19)14-10)12-2-16(7)9-6(18)5(17)3(28-9)1-27-32(25,26)29-31(23,24)15-30(20,21)22/h2-3,5-6,9,17-18H,1H2,(H,25,26)(H3,11,13,14,19)(H4,15,20,21,22,23,24)/t3-,5-,6-,9-/m1/s1
Release date: 2024-02-07