satarupa22/MacromolecularLigandDB huggingface dataset:
CDK8-CYCC IN COMPLEX WITH 5-{5-Chloro-4-[1-(2-methoxy-ethyl)-1,8-diaza-spiro[4.5]dec-8-yl]-pyridin-3-yl}-1-methyl-1,3-dihydro-benzo[c]isothiazole 2,2-dioxide (PDB entry 5HBH)
Macromolecule: Cyclin-dependent kinase 8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.22
Sequence length: 364 residues
Sequence: DKMDYDFKVKLSSERERVEDLFEYEGCKVGRGTYGHVYKAKRKDGKDDKDYALKQIEGTGISMSACREIALLRELKHPNVISLQKVFLSHADRKVWLLFDYAEHDLWHIIKFHRASKANKKPVQLPRGMVKSLLYQILDGIHYLHANWVLHRDLKPANILVMGEGPERGRVKIADMGFARLFNSPLKPLADLDPVVVTFWYRAPELLLGARHYTKAIDIWAIGCIFAELLTSEPIFHCRQEDIKTSNPYHHDQLDRIFNVMGFPADKDWEDIKKMPEHSTLMKDFRRNTYTNCSLIKYMEKHKVKPDSKAFHLLQKLLTMDPIKRITSEQAMQDPYFLEDPLPTSDVFAGCQIPYPKREFLTEE
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2338
R free: 0.2683
Average B factor: 67.492
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.9
Crystallization temperature (K): 293
Crystal growth procedure: RESERVOIR SOLUTION : pH 6.90
Matthews coefficient: 2.95
Solvent content (%): 58.31
Ligand: 5-[5-chloranyl-4-[1-(2-methoxyethyl)-1,8-diazaspiro[4.5]decan-8-yl]pyridin-3-yl]-1-methyl-3~{H}-2,1-benzothiazole 2,2-dioxide (5Y7)
Ligand formula: C24 H31 Cl N4 O3 S
Ligand molecular weight: 491.046
Ligand SMILES: CN1c2ccc(cc2CS1(=O)=O)c3cncc(c3N4CCC5(CCCN5CCOC)CC4)Cl
Ligand InChI: InChI=1S/C24H31ClN4O3S/c1-27-22-5-4-18(14-19(22)17-33(27,30)31)20-15-26-16-21(25)23(20)28-10-7-24(8-11-28)6-3-9-29(24)12-13-32-2/h4-5,14-16H,3,6-13,17H2,1-2H3
Release date: 2016-02-03
Crystal structure of the PDE5A1 catalytic domain in complex with novel inhibitors (PDB entry 4OEX)
Macromolecule: cGMP-specific 3',5'-cyclic phosphodiesterase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.4.35
Sequence length: 347 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMEETRELQSLAAAVVPSAQTLKITDFSFSDFELSDLETALCTIRMFTDLNLVQNFQMKHEVLCRWILSVKKNYRKNVAYHNWRHAFNTAQCMFAALKAGKIQNKLTDLEILALLIAALSHDLDHRGVNNSYIQRSEHPLAQLYCHSIMEHHHFDQCLMILNSPGNQILSGLSIEEYKTTLKIIKQAILATDLALYIKRRGEFFELIRKNQFNLEDPHQKELFLAMLMTACDLSAITKPWPIQQRIAELVATEFFDQGDRERKELNIEPTDLMNREKKNKIPSMQVGFIDAICLQLYEALTHVSEDCFPLLDGCRKNRQKWQALAEQQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.14
R work: 0.1912
R free: 0.2396
Average B factor: 39.59
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 19-20%(w/v)PEG 3350, 200mM MgSO4, 100mM Tris-HCl, pH 7.5, vapor diffusion, hanging drop, temperature 293K
Matthews coefficient: 2.6
Solvent content (%): 52.76
Ligand: 6-ethyl-2-{5-[(4-methylpiperazin-1-yl)sulfonyl]-2-propoxyphenyl}pyrimidin-4(3H)-one (5EO)
Ligand formula: C20 H28 N4 O4 S
Ligand molecular weight: 420.526
Ligand SMILES: CCCOc1ccc(cc1C2=NC(=CC(=O)N2)CC)S(=O)(=O)N3CCN(CC3)C
Ligand InChI: InChI=1S/C20H28N4O4S/c1-4-12-28-18-7-6-16(29(26,27)24-10-8-23(3)9-11-24)14-17(18)20-21-15(5-2)13-19(25)22-20/h6-7,13-14H,4-5,8-12H2,1-3H3,(H,21,22,25)
Release date: 2015-04-01
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z104479710 (PDB entry 7G8E)
Macromolecule: Transforming protein RhoA
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.6.5.2
Sequence length: 185 residues
Sequence: SMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLRPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVKPEEGRDMANRIGAFGYMECSAKTKDGVREVFEMATRAALQARRG
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.79
R work: 0.1981
R free: 0.2231
Average B factor: 34
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.54
Solvent content (%): 51.64
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: 2023-07-12
Crystal structure of human carbonic anhydrase II in complex with the inhibitor 4-Pyridin-3-yl-benzenesulfonamide (PDB entry 5N25)
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): 1.4
R work: 0.1722
R free: 0.1991
Average B factor: 14.02
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 8
Crystallization temperature (K): 296
Crystal growth procedure: 1.5 M sodium citrate, Tris 50 mM
Matthews coefficient: 2.07
Solvent content (%): 40.65
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: 2017-12-27
ARHGEF2 PanDDA analysis group deposition -- ARHGEF2 and RhoA in complex with Z1079512010 (PDB entry 7G82)
Macromolecule: Rho guanine nucleotide exchange factor 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 245 residues
Sequence: SMEMDEKDFAADSWSLAVDSSFLQQHKKEVMKQQDVIYELIQTELHHVRTLKIMTRLFRTGMLEELHLEPGVVQGLFPCVDELSDIHTRFLSQLLERRRQALCPGSTRNFVIHRLGDLLISQFSGPSAEQMCKTYSEFCSRHSKALKLYKELYARDKRFQQFIRKVTRPAVLKRHGVQECILLVTQRITKYPLLISRILQHSHGIEEERQDLTTALGLVKELLSNVDEGIYQLEKGARLQEIYNR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.409
R work: 0.1877
R free: 0.2092
Average B factor: 27.26
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 293
Crystal growth procedure: 100 mM Tris, 2.6M sodium formate
Matthews coefficient: 2.51
Solvent content (%): 51.07
Ligand: 6-methyl-2-[(3-methyl-1,2-oxazol-5-yl)methyl]pyridazin-3(2H)-one (UWS)
Ligand formula: C10 H11 N3 O2
Ligand molecular weight: 205.213
Ligand SMILES: Cc1cc(on1)CN2C(=O)C=CC(=N2)C
Ligand InChI: InChI=1S/C10H11N3O2/c1-7-3-4-10(14)13(11-7)6-9-5-8(2)12-15-9/h3-5H,6H2,1-2H3
Release date: 2023-07-12
Human cyclophilin A at 100K, Data set 2 (PDB entry 5KUN)
Macromolecule: Peptidyl-prolyl cis-trans isomerase A
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGEKFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADCGQLE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.7
R work: 0.1737
R free: 0.2084
Average B factor: 17.749
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 291
Crystal growth procedure: CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
Matthews coefficient: 2.78
Solvent content (%): 55.71
Release date: 2016-08-10
Crystal structure of human Carbonic anhydrase II in complex with (R)-4-(2-benzyl-4-methylpiperazin-1-yl)benzenesulfonamide (PDB entry 6RG4)
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): 1.25
R work: 0.1556
R free: 0.2002
Average B factor: 18.175
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.3
Crystallization temperature (K): 286
Crystal growth procedure: 1.6 sodium citrate
Matthews coefficient: 2.08
Solvent content (%): 40.91
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: 2020-05-13
FGFR1 kinase domain with a covalent inhibitor 10h (PDB entry 8XZ7)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 310 residues
Sequence: GPAGVSEYELPEDPRWELPRDRLVLGKPLGEGCFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.75
R work: 0.1865
R free: 0.2251
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 18% PEG 8000, 0.2 M Li2SO4, and 0.1 M MES, pH 6.5
Matthews coefficient: 2.37
Solvent content (%): 48.05
Ligand: 5-azanyl-3-[2-[4,6-bis(fluoranyl)-2-methyl-3~{H}-benzimidazol-5-yl]ethynyl]-1-[[3-(prop-2-enoylamino)phenyl]methyl]pyrazole-4-carboxamide (A1LWW)
Ligand formula: C24 H19 F2 N7 O2
Ligand molecular weight: 475.45
Ligand SMILES: Cc1[nH]c2c(n1)cc(c(c2F)C#Cc3c(c(n(n3)Cc4cccc(c4)NC(=O)C=C)N)C(=O)N)F
Ligand InChI: InChI=1S/C24H19F2N7O2/c1-3-19(34)31-14-6-4-5-13(9-14)11-33-23(27)20(24(28)35)17(32-33)8-7-15-16(25)10-18-22(21(15)26)30-12(2)29-18/h3-6,9-10H,1,11,27H2,2H3,(H2,28,35)(H,29,30)(H,31,34)
Release date: 2024-06-26
Ternary complex crystal structure of DNA polymerase Beta with A:C mismatch at the primer terminus (PDB entry 5J2A)
Macromolecule: DNA polymerase beta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 335 residues
Sequence: MSKRKAPQETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEKEYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDSEKDIFDYIQWKYREPKDRSE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2247
R free: 0.2957
Average B factor: 27.1632
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350, 50 mM Imidazole, 350 mM Sodium Acetate
Matthews coefficient: 2.27
Solvent content (%): 45.83
Ligand: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE (DUP)
Ligand formula: C9 H16 N3 O13 P3
Ligand molecular weight: 467.157
Ligand SMILES: C1C(C(OC1N2C=CC(=O)NC2=O)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O13P3/c13-5-3-8(12-2-1-7(14)10-9(12)15)24-6(5)4-23-26(16,17)11-27(18,19)25-28(20,21)22/h1-2,5-6,8,13H,3-4H2,(H,10,14,15)(H2,20,21,22)(H3,11,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2016-10-26
Plk1 polo-box domain bound to HPV18 L2 residues 209-215 with pThr213 (PDB entry 8JOQ)
Macromolecule: Serine/threonine-protein kinase PLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 226 residues
Sequence: GHDCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSR
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.796
R work: 0.2056
R free: 0.2497
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 0.1M malate MES Tris buffer pH 6.5, 25% polyethylene glycol 1500
Matthews coefficient: 2.09
Solvent content (%): 41.25
Release date: 2023-10-11
Structure of Maternal Embryonic Leucine Zipper Kinase (PDB entry 5TVT)
Macromolecule: Maternal embryonic leucine zipper kinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 334 residues
Sequence: GSKDYDELLKYYELHETIGTGGFAKVKLACHILTGEMVAIKIMDKNTLGSDLPRIKTEIEALKNLRHQHICQLYHVLETANKIFMVLEYCPGGELFDYIISQDRLSEEETRVVFRQIVSAVAYVHSQGYAHRDLKPENLLFDEYHKLKLIDFGLCAKPKGNKDYHLQTCCGSLAYAAPELIQGKSYLGSEADVWSMGILLYVLMCGFLPFDDDNVMALYKKIMRGKYDVPKWLSPSSILLLQQMLQVDPKKRISMKNLLNHPWIMQDYNYPVEWQSKNPFIHLDDDCVTELSVHHRNNRQTMEDLISLWQYDHLTATYLLLLAKKARGKPVRLR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.28
R work: 0.1897
R free: 0.2294
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 24% PEG3350, 0.1 M MgCl, 0.1M HEPES pH 7.0
Matthews coefficient: 2.58
Solvent content (%): 52.27
Ligand: 9-(3,5-dichloro-4-hydroxyphenyl)-1-{trans-4-[(dimethylamino)methyl]cyclohexyl}-3-methyl-3,4-dihydropyrimido[5,4-c][1,5]naphthyridin-2(1H)-one (7LV)
Ligand formula: C26 H29 Cl2 N5 O2
Ligand molecular weight: 514.447
Ligand SMILES: CN1Cc2cnc3ccc(nc3c2N(C1=O)C4CCC(CC4)CN(C)C)c5cc(c(c(c5)Cl)O)Cl
Ligand InChI: InChI=1S/C26H29Cl2N5O2/c1-31(2)13-15-4-6-18(7-5-15)33-24-17(14-32(3)26(33)35)12-29-22-9-8-21(30-23(22)24)16-10-19(27)25(34)20(28)11-16/h8-12,15,18,34H,4-7,13-14H2,1-3H3/t15-,18-
Release date: 2017-11-15
CRYSTAL STRUCTURE OF BACE-1 IN COMPLEX WITH Pep#3 (PDB entry 5MBW)
Macromolecule: Beta-secretase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.23.46
Sequence length: 409 residues
Sequence: ETDEEPEEPGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDEST
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.16289
R free: 0.21553
Average B factor: 73.289
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 273
Crystal growth procedure: 0.1M sodium chloride, 0.1M HEPES, 1.6M ammonium sulfate, 0.098M HEGA-9
Matthews coefficient: 3.92
Solvent content (%): 68.66
Ligand: CHLORIDE ION (CL)
Ligand formula: Cl
Ligand molecular weight: 35.453
Ligand SMILES: [Cl-]
Ligand InChI: InChI=1S/ClH/h1H/p-1
Release date: 2017-09-27
The Crystal Structure of polo-box domain of PLK1 from Biortus. (PDB entry 8XB9)
Macromolecule: Serine/threonine-protein kinase PLK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.21
Sequence length: 237 residues
Sequence: GAHMDCHLSDMLQQLHSVNASKPSERGLVRQEEAEDPACIPIFWVSKWVDYSDKYGLGYQLCDNSVGVLFNDSTRLILYNDGDSLQYIERDGTESYLTVSSHPNSLMKKITLLKYFRNYMSEHLLKAGANITPREGDELARLPYLRTWFRTRSAIILHLSNGSVQINFFQDHTKLILCPLMAAVTYIDEKRDFRTYRLSLLEEYGCCKELASRLRYARTMVDKLLSSRSASNRLKAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.95
R work: 0.1885
R free: 0.2448
Average B factor: 44.155
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 31% PEG3350, 0.1M Bis Tris pH 5.8
Matthews coefficient: 1.98
Solvent content (%): 37.98
Ligand: 1,2-ETHANEDIOL (EDO)
Ligand formula: C2 H6 O2
Ligand molecular weight: 62.068
Ligand SMILES: C(CO)O
Ligand InChI: InChI=1S/C2H6O2/c3-1-2-4/h3-4H,1-2H2
Release date: 2023-12-27
IRAK4 IN COMPLEX WITH COMPOUND #3 (PDB entry 8DKS)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 460 residues
Sequence: MNKPITPSTYVRCLNVGLIRKLSDFIDPQEGWKKLAVAIKKPSGDDRYNQFHIRRFEALLQTGKSPTSELLFDWGTTNCTVGDLVDLLIQNEFFAPASLLLPDAVPKTANTLPSKEAITVQQKQMPFCDKDRTLMTPVQNLEQSYMPPDSSSPENKSLEVSDTRFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMTAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.45
R work: 0.21375
R free: 0.26716
Average B factor: 39.1074
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: The purified protein was used in crystallisation trials employing
both, a standard screen with approximately 1200 different conditions,
as well as crystallisation conditions identified using literature
data. Conditions initially obtained have been optimised using standard
strategies, systematically varying parameters critically influencing
crystallisation, such as temperature, protein concentration,
drop ratio, and others. These conditions were also refined by systematically
varying pH or precipitant concentrations.
Matthews coefficient: 2.79
Solvent content (%): 55.92
Ligand: (1S,2S,3R,4R)-3-({2-[3-(pyrrolidine-1-carbonyl)anilino]thieno[3,2-d]pyrimidin-4-yl}amino)bicyclo[2.2.1]hept-5-ene-2-carboxamide (SO9)
Ligand formula: C25 H26 N6 O2 S
Ligand molecular weight: 474.578
Ligand SMILES: c1cc(cc(c1)Nc2nc3ccsc3c(n2)NC4C5CC(C4C(=O)N)C=C5)C(=O)N6CCCC6
Ligand InChI: InChI=1S/C25H26N6O2S/c26-22(32)19-14-6-7-15(12-14)20(19)29-23-21-18(8-11-34-21)28-25(30-23)27-17-5-3-4-16(13-17)24(33)31-9-1-2-10-31/h3-8,11,13-15,19-20H,1-2,9-10,12H2,(H2,26,32)(H2,27,28,29,30)/t14-,15+,19+,20-/m1/s1
Release date: 2022-08-03
INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2856434858 (PDB entry 5RXU)
Macromolecule: Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.86
Sequence length: 463 residues
Sequence: SMEQPEPDMITIFIGTWNMGNAPPPKKITSWFLSKGQGKTRDDSADYIPHDIYVIGTQEDPLSEKEWLEILKHSLQEITSVTFKTVAIHTLWNIRIVVLAKPEHENRISHICTDNVKTGIANTLGNKGAVGVSFMFNGTSLGFVNSHLTSGSEKKLRRNQNYMNILRFLALGDKKLSPFNITHRFTHLFWFGDLNYRVDLPTWEAETIIQKIKQQQYADLLSHDQLLTERREQKVFLHFEEEEITFAPTYRFERLTRDKYAYTKQKATGMKYNLPSWCDRVLWKSYPLVHVVCQSYGSTSDIMTSDHSPVFATFEAGVTSQFVSKNGPGTVDSQGQIEFLRCYATLKTKSQTKFYLEFHSSCLESFVKSQEGENEEGSEGELVVKFGETLPKLKPIISDPEYLLDQHILISIKSSDSDESYGEGCIALRLEATETQLPIYTPLTHHGELTGHFQGEIKLQTSQ
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.181
R free: 0.2132
Average B factor: 25.676
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 30 mM sodium nitrate, 30 mM dibasic sodium phosphate, 30 mM ammonium sulfate, 100 mM MES/imidazole, pH 6.5, 20% PEG500 MME, 10% PEG20000
Matthews coefficient: 2.06
Solvent content (%): 40.36
Ligand: (3R)-1-[(4-chlorophenyl)methyl]pyrrolidin-3-ol (WKJ)
Ligand formula: C11 H14 Cl N O
Ligand molecular weight: 211.688
Ligand SMILES: c1cc(ccc1CN2CCC(C2)O)Cl
Ligand InChI: InChI=1S/C11H14ClNO/c12-10-3-1-9(2-4-10)7-13-6-5-11(14)8-13/h1-4,11,14H,5-8H2/t11-/m1/s1
Release date: 2020-11-11
BTK in complex with 18A (PDB entry 7R60)
Macromolecule: Tyrosine-protein kinase BTK
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 271 residues
Sequence: GLGYGSWEIDPKDLTFLKELGTGQFGVVKYGKWRGQYDVAIKMIKEGSMSEDEFIEEAKVMMNLSHEKLVQLYGVCTKQRPIFIITEYMANGCLLNYLREMRHRFQTQQLLEMCKDVCEAMEYLESKQFLHRDLAARNCLVNDQGVVKVSDFGLSRYVLDDEYTSSVGSKFPVRWSPPEVLMYSKFSSKSDIWAFGVLMWEIYSLGKMPYERFTNSETAEHIAQGLRLYRPHLASEKVYTIMYSCWHEKADERPTFKILLSNILDVMDEES
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.94
R work: 0.216
R free: 0.2646
Average B factor: 15.228
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 295
Crystal growth procedure: 20% PEG 3350,
0.1 M Bis Tris Propane pH 7.5,
0.2 M Sodium acetate trihydrate
Matthews coefficient: 2.5
Solvent content (%): 50.87
Ligand: 2-(4-phenoxyphenoxy)-5-[(3R)-1-(prop-2-enoyl)piperidin-3-yl]pyridine-3-carboxamide (2IE)
Ligand formula: C26 H27 N3 O4
Ligand molecular weight: 445.51
Ligand SMILES: CCC(=O)N1CCCC(C1)c2cc(c(nc2)Oc3ccc(cc3)Oc4ccccc4)C(=O)N
Ligand InChI: InChI=1S/C26H27N3O4/c1-2-24(30)29-14-6-7-18(17-29)19-15-23(25(27)31)26(28-16-19)33-22-12-10-21(11-13-22)32-20-8-4-3-5-9-20/h3-5,8-13,15-16,18H,2,6-7,14,17H2,1H3,(H2,27,31)/t18-/m0/s1
Release date: 2021-10-06
Crystal structure of indoleamine 2,3-dioxygenagse 1 (IDO1) in complex with compound 36 (PDB entry 6KPS)
Macromolecule: Indoleamine 2,3-dioxygenase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.13.11.52
Sequence length: 403 residues
Sequence: MAHAMENSWTISKEYHIDEEVGFALPNPQENLPDFYNDWMFIAKHLPDLIESGQLRERVEKLNMLSIDHLTDHKSQRLARLVLGCITMAYVWGKGHGDVRKVLPRNIAVPYCQLSKKLELPPILVYADCVLANWKKKDPNKPLTYENMDVLFSFRDGDCSKGFFLVSLLVEIAAASAIKVIPTVFKAMQMQERDTLLKALLEIASCLEKALQVFHQIHDHVNPKAFFSVLRIYLSGWKGNPQLSDGLVYEGFWEDPKEFAGGSAGQSSVFQCFDVLLGIQQTAGGGHAAQFLQDMRRYMPPAHRNFLCSLESNPSVREFVLSKGDAGLREAYDACVKALVSLRSYHLQIVTKYILIPASQQPKENKTSEDPSKLEAKGTGGTDLMNFLKTVRSTTEKSLLKEG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.249
R work: 0.2038
R free: 0.2426
Average B factor: 56.2609
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: PEG3350, Ammonium Fluoride, MES
Matthews coefficient: 2.85
Solvent content (%): 56.91
Ligand: PROTOPORPHYRIN IX CONTAINING FE (HEM)
Ligand formula: C34 H32 Fe N4 O4
Ligand molecular weight: 616.487
Ligand SMILES: Cc1c2n3c(c1CCC(=O)O)C=C4C(=C(C5=[N]4[Fe]36[N]7=C(C=C8N6C(=C5)C(=C8C)C=C)C(=C(C7=C2)C)C=C)C)CCC(=O)O
Ligand InChI: InChI=1S/C34H34N4O4.Fe/c1-7-21-17(3)25-13-26-19(5)23(9-11-33(39)40)31(37-26)16-32-24(10-12-34(41)42)20(6)28(38-32)15-30-22(8-2)18(4)27(36-30)14-29(21)35-25;/h7-8,13-16H,1-2,9-12H2,3-6H3,(H4,35,36,37,38,39,40,41,42);/q;+2/p-2/b25-13-,26-13-,27-14-,28-15-,29-14-,30-15-,31-16-,32-16-;
Release date: 2020-03-25
Structure of Cyclophilin D Peptidyl-Prolyl Isomerase Domain bound to Macrocyclic Inhibitor B2 (PDB entry 7TGV)
Macromolecule: Peptidyl-prolyl cis-trans isomerase F, mitochondrial
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 5.2.1.8
Sequence length: 164 residues
Sequence: GNPLVYLDVDANGKPLGRVVLELKADVVPKTAENFRALCTGEKGFGYKGSTFHRVIPSFMCQAGDFTNHNGTGGKSIYGSRFPDENFTLKHVGPGVLSMANAGPNTNGSQFFICTIKTDWLDGKHVVFGHVIEGMDVVKKIESFGSKSGRTSKKIVITDCGQLS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.46
R work: 0.1654
R free: 0.1786
Average B factor: 12.06
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.3
Crystallization temperature (K): 298
Crystal growth procedure: 28% PEG 3350
0.5 M KH2PO4
Protein and inhibitor were mixed in ratio 1:3
1 uL of protein:inhibitor complex was mixed with 1 uL mother liquor
Matthews coefficient: 2.44
Solvent content (%): 49.6
Ligand: (4S,7S,11R,13E,19S)-N-[2-(2-aminoethoxy)ethyl]-7-benzyl-4-[([1,1'-biphenyl]-4-yl)methyl]-3,6,12,15,21-pentaoxo-1,3,4,5,6,7,8,9,10,12,15,16,17,18,19,20,21,22-octadecahydro-2H-7,11-methano-2,5,11,16,20-benzopentaazacyclotetracosine-19-carboxamide (I3X)
Ligand formula: C49 H57 N7 O7
Ligand molecular weight: 856.02
Ligand SMILES: c1ccc(cc1)CC23CCCN(C2)C(=O)C=CC(=O)NCCC(NC(=O)Cc4ccccc4CNC(=O)C(NC3=O)Cc5ccc(cc5)c6ccccc6)C(=O)NCCOCCN
Ligand InChI: InChI=1S/C49H57N7O7/c50-24-28-63-29-26-52-46(60)41-22-25-51-43(57)20-21-45(59)56-27-9-23-49(34-56,32-36-10-3-1-4-11-36)48(62)55-42(30-35-16-18-38(19-17-35)37-12-5-2-6-13-37)47(61)53-33-40-15-8-7-14-39(40)31-44(58)54-41/h1-8,10-21,41-42H,9,22-34,50H2,(H,51,57)(H,52,60)(H,53,61)(H,54,58)(H,55,62)/b21-20+/t41-,42-,49-/m0/s1
Release date: 2022-08-24