satarupa22/MacromolecularLigandDB huggingface dataset:
Crystal structure of human tryptophan hydroxylase 1 in complex with inhibitor KM-05-193 (PDB entry 7ZII)
Macromolecule: Tryptophan 5-hydroxylase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.16.4
Sequence length: 326 residues
Sequence: MKHHHHHHHGAAGTSLYKKAGENLYFQGSVPWFPKKISDLDHCANRVLMYGSELDADHPGFKDNVYRKRRKYFADLAMNYKHGDPIPKVEFTEEEIKTWGTVFQELNKLYPTHACREYLKNLPLLSKYCGYREDNIPQLEDVSNFLKERTGFSIRPVAGYLSPRDFLSGLAFRVFHCTQYVRHSSDPFYTPEPDTCHELLGHVPLLAEPSFAQFSQEIGLASLGASEEAVQKLATCYFFTVEFGLCKQDGQLRVFGAGLLSSISELKHALSGHAKVKPFDPKITCKQECLITTFQDVYFVSESFEDAKEKMREFTKTIKRPFGVKY
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.62800050605
R work: 0.16709833574
R free: 0.191912784114
Average B factor: 25.8363252539
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293.15
Crystal growth procedure: 20% w/v PEG 3350, 200 mM potassium formate pH 7.3
Matthews coefficient: 2.14
Solvent content (%): 42.45
Ligand: FE (III) ION (FE)
Ligand formula: Fe
Ligand molecular weight: 55.845
Ligand SMILES: [Fe+3]
Ligand InChI: InChI=1S/Fe/q+3
Release date: 2022-09-07
Structure of human DNA polymerase eta complexed with N7MG in the template base paired with incoming non-hydrolyzable CTP (PDB entry 6UI2)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.35
R work: 0.1704
R free: 0.2374
Average B factor: 24.9462
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 298
Crystal growth procedure: 0.1M MES (pH 5.5), 5 mM MgCl2, and 15 to 20 % PEG 2K-MME
Matthews coefficient: 2.1
Solvent content (%): 41.48
Ligand: 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine (0KX)
Ligand formula: C9 H17 N4 O12 P3
Ligand molecular weight: 466.172
Ligand SMILES: C1C(C(OC1N2C=CC(=NC2=O)N)COP(=O)(NP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H17N4O12P3/c10-7-1-2-13(9(15)11-7)8-3-5(14)6(24-8)4-23-26(16,17)12-27(18,19)25-28(20,21)22/h1-2,5-6,8,14H,3-4H2,(H2,10,11,15)(H2,20,21,22)(H3,12,16,17,18,19)/t5-,6+,8+/m0/s1
Release date: 2020-01-15
Crystal structure of FGFR4 kinase domain with 8zc (PDB entry 8KH7)
Macromolecule: Fibroblast growth factor receptor 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 311 residues
Sequence: GPLLAGLVSLDLPLDPLWEFPRDRLVLGKPLGEGCFGQVVRAEAFGMDPARPDQASTVAVKMLKDNASDKDLADLVSEMEVMKLIGRHKNIINLLGVCTQEGPLYVIVECAAKGNLREFLRARRPPGPDLSPDGPRSSEGPLSFPVLVSCAYQVARGMQYLESRKCIHRDLAARNVLVTEDNVMKIADFGLARGVHHIDYYKKTSNGRLPVKWMAPEALFDEVYTHQSDVWSFGILLWEIFTLGGSPYPGIPVEELFSLLREGHRMDRPPHCPPELYGLMRECWHAAPSQRPTFKQLVEALDKVLLAVSEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.52
R work: 0.1644
R free: 0.1948
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.1 M Bis-Tris (pH 4.5), 0.2 M Li2SO4, 16-19% PEG 3350
Matthews coefficient: 2.23
Solvent content (%): 44.79
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: 2024-07-31
Ternary complex crystal structure of DNA polymerase Beta with a dideoxy terminated primer with CHF-R/S isomers, beta, gamma dTTP analogue (PDB entry 6CTK)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*AP*GP*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: Homo sapiens
Sequence length: 16 residues
Sequence: CCGACAGCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.153
R work: 0.1787
R free: 0.244
Average B factor: 38.6754
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 16-18% PEG 3350
Matthews coefficient: 2.28
Solvent content (%): 46.02
Ligand: SODIUM ION ()
Ligand formula: Na
Ligand molecular weight: 22.99
Ligand SMILES: [Na+]
Ligand InChI: InChI=1S/Na/q+1
Release date: 2018-06-20
LSD1-CoREST in complex N-formyl FAD and SNAG peptide (PDB entry 8FDV)
Macromolecule: REST corepressor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 144 residues
Sequence: GPLGSPEFRAKRKPPKGMFLSQEDVEAVSANATAATTVLRQLDMELVSVKRQIQNIKQTNSALKEKLDGGIEPYRLPEVIQKCNARWTTEEQLLAVQAIRKYGRDFQAISDVIGNKSVVQVKNFFVNYRRRFNIDEVLQEWEAE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.95
R work: 0.2162
R free: 0.252
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.2 Na/K Tartrate, 100 mM ADA pH 6.5
Matthews coefficient: 5.56
Solvent content (%): 77.89
Ligand: [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate (HUF)
Ligand formula: C28 H35 N9 O16 P2
Ligand molecular weight: 815.576
Ligand SMILES: Cc1cc2c(cc1C)N(C3=C(N2CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O)NC(=O)NC3=O)C=O
Ligand InChI: InChI=1S/C28H35N9O16P2/c1-11-3-13-14(4-12(11)2)37(10-38)19-25(33-28(45)34-26(19)44)35(13)5-15(39)20(41)16(40)6-50-54(46,47)53-55(48,49)51-7-17-21(42)22(43)27(52-17)36-9-32-18-23(29)30-8-31-24(18)36/h3-4,8-10,15-17,20-22,27,39-43H,5-7H2,1-2H3,(H,46,47)(H,48,49)(H2,29,30,31)(H2,33,34,44,45)/t15-,16+,17+,20-,21+,22+,27+/m0/s1
Release date: 2024-06-12
Fragment-Based Drug Discovery Targeting Inhibitor of Apoptosis Proteins: Compound 2 (PDB entry 5C0L)
Macromolecule: E3 ubiquitin-protein ligase XIAP
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 6.3.2
Sequence length: 110 residues
Sequence: GSHMNFPNSTNLPRNPSMADYEARIFTFGTWIYSVNKEQLARAGFYALGEGDKVKCFHCGGGLTDWKPSEDPWEQHAKWYPGCKYLLEQKGQEYINNIHLTHSLEECLVR
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.6
R work: 0.19979
R free: 0.23234
Average B factor: 45.118
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 3.9M NaCl, 0.1M HEPES/NaOHpH=7.5
Matthews coefficient: 2.32
Solvent content (%): 47
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: 2015-08-12
Structure of the catalytic domain of USP28 (insertion deleted) bound to Ubiquitin-PA (PDB entry 6HEI)
Macromolecule: Ubiquitin carboxyl-terminal hydrolase 28,Ubiquitin carboxyl-terminal hydrolase 28
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.19.12
Sequence length: 382 residues
Sequence: GPNPNDWRRVDGWPVGLKNVGNTCWFSAVIQSLFQLPEFRRLVLSYSLPQNVLENCRSHTEKRNIMFMQELQYLFALMMGSNRKFVDPSAALDLLKGAFRSSEEQQQDVSEFTHKLLDWLEDAFQLAVNVNSPRNKSENPMVQLFYGTFLTEGVREGKPFCNNETFGQYPLQVNGYRNLDECLEGAMVEGDVELLPSDHSVKYGQERWFTKLPPVLTFELSRFEFNQSLGQPEKIHNKLEFPQIIYMDRYMYGSGSGSRQVPYRLHAVLVHEGQANAGHYWAYIYNQPRQSWLKYNDISVTESSWEEVERDSYGGLRNVSAYCLMYINDKLPYFNAEAAPTESDQMSEVEALSVELKHYIQEDNWRFEQEVEEWEEEQSCKI
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.64
R work: 0.1857
R free: 0.2138
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8
Crystallization temperature (K): 291
Crystal growth procedure: 22% (w/v) PEG 3350, 300 mM potassium sodium tartrate
Matthews coefficient: 1.97
Solvent content (%): 37.5
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: 2019-03-27
Secreted phospholipase A2 type X in complex with ligand (PDB entry 6G5J)
Macromolecule: Group 10 secretory phospholipase A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.4
Sequence length: 165 residues
Sequence: MGPLPVCLPIMLLLLLPSLLLLLLLPGPGSGEASRILRVHRRGILELAGTVGCVGPRTPIAYMKYGCFCGLGGHGQPRDAIDWCCHGHDCCYTRAEEAGCSPKTERYSWQCVNQSVLCGPAENKCQELLCKCDQEIANCLAQTEYNLKYLFYPQFLCEPDSPKCD
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.19392
R free: 0.22779
Average B factor: 23.567
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 295
Crystal growth procedure: 37-45% PEG400
0.1M bis-Tris pH 5.6-5.9
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2018-09-05
Metala-Carborane di-ethyl-sulfonamide (trans isomer) in complex with CA IX mimic (PDB entry 6YKC)
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): 1.2
R work: 0.1474
R free: 0.179
Average B factor: 18.981
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: 2.07
Solvent content (%): 40.68
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: 2020-09-09
Crystal Structure of Jarid1a PHD finger bound to histone H3C4me3 peptide (PDB entry 5C11)
Macromolecule: H3 peptide
Type: Protein, polypeptide(L)
Source organism: synthetic construct
Sequence length: 10 residues
Sequence: ARTXQTARKS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.803
R work: 0.2455
R free: 0.2789
Average B factor: 95.2107
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.02 M sodium l-glutamate, 0.02 M dl-alanine, 0.02 M glycine, 0.02 M dl-lysine HCl, 0.02 M dl-serine, 0.1 M Tris, 0.1 M Bicine, PH8.5, 12.5% MPD, 12.5%  PEG 1K, 12.5%  PEG 3350
Matthews coefficient: 3.67
Solvent content (%): 66.47
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: 2015-11-25
CRYSTAL STRUCTURE OF JAK3 KINASE DOMAIN IN COMPLEX WITH A PYRROLOPYRIDAZINE INHIBITOR (PDB entry 5VO6)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 293 residues
Sequence: GPASQDPTIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGSERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLWS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.209
R free: 0.284
Average B factor: 45.47
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 300
Matthews coefficient: 2.32
Solvent content (%): 47.05
Ligand: 4-{[(1R,3S)-3-amino-2,2,3-trimethylcyclopentyl]amino}-6-phenylpyrrolo[1,2-b]pyridazine-3-carboxamide (9J4)
Ligand formula: C22 H27 N5 O
Ligand molecular weight: 377.483
Ligand SMILES: CC1(C(CCC1(C)N)Nc2c3cc(cn3ncc2C(=O)N)c4ccccc4)C
Ligand InChI: InChI=1S/C22H27N5O/c1-21(2)18(9-10-22(21,3)24)26-19-16(20(23)28)12-25-27-13-15(11-17(19)27)14-7-5-4-6-8-14/h4-8,11-13,18,26H,9-10,24H2,1-3H3,(H2,23,28)/t18-,22+/m1/s1
Release date: 2017-05-31
Crystal structure of the catalytic domain of Human MMP12 in complex with a carboxylate inhibitor related to RXP470 (PDB entry 5CXA)
Macromolecule: Macrophage metalloelastase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.4.24.65
Sequence length: 159 residues
Sequence: MGPVWRKHYITYRINNYTPDMNREDVDYAIRKAFQVWSNVTPLKFSKINTGMADILVVFARGAHGDDHAFDGKGGILAHAFGPGSGIGGDAHFDEDEFWTTHSGGTNLFLTAVHEIGHSLGLGHSSDPKAVMFPTYAYVDINTFRLSADDIRGIQSLYG
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.3
R work: 0.1403
R free: 0.181
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 10
Crystallization temperature (K): 293
Crystal growth procedure: Protein:  hMMP12 F171D K241A at 608 micro-M + 10 milli-M AHA + 0.552 milli-M inhibitor. precipitant: 26% PEG4000, 3% dioxane, 0.114 M TRIS pH 10. cryoprotectant: 10 % diethylene glycol + 5 % glycerol + 10 % 2,3-butanediol + 5 % 1,4-dioxane, 25% PEG 6K, 0.1 M TRIS-HCl, pH 8.0
Matthews coefficient: 2.29
Solvent content (%): 46.18
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: 2016-08-10
Crystal Structure of the Human vaccinia-related kinase bound to a phenyl-pteridinone inhibitor (PDB entry 6BTW)
Macromolecule: Serine/threonine-protein kinase VRK1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 364 residues
Sequence: SMRVKAAQAGRQSSAKRHLAEQFAVGEIITDMAAAAWKVGLPIGQGGFGCIYLADMNSSESVGSDAPCVVKVEPSDNGPLFTELKFYQRAAKPEQIQKWIRTRKLKYLGVPKYWGSGLHDKNGKSYRFMIMDRFGSDLQKIYEANAKRFSRKTVLQLSLRILDILEYIHEHEYVHGDIKASNLLLNYKNPDQVYLVDYGLAYRYCPEGVHKAYAADPKRCHDGTIEFTSIDAHNGVAPSRRGDLEILGYCMIQWLTGHLPWEDNLKDPKYVRDSKIRYRENIASLMDKCFPAANAPGEIAKYMETVKLLDYTEKPLYENLRDILLQGLKAIGSKDDGKLDLSVVENGGLKAKTITKKRAAEIEE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.9
R work: 0.18197
R free: 0.2147
Average B factor: 29.63
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 22% PEG3350, 0.02M Lithium Sulfate, 0.1M Buffer system SBG pH 7.0
Matthews coefficient: 2.65
Solvent content (%): 53.62
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: 2017-12-20
Crystal structure of human secreted phospholipase A2 group IIE (PDB entry 5WZM)
Macromolecule: Group IIE secretory phospholipase A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.1.4
Sequence length: 121 residues
Sequence: VQFGVMIEKMTGKSALQYNDYGCYCGIGGSHWPVDQTDWCCHAHDCCYGRLEKLGCEPKLEKYLFSVSERGIFCAGRTTCQRLTCECDKRAALCFRRNLGTYNRKYAHYPNKLCTGPTPPC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2
R work: 0.1847
R free: 0.226
Average B factor: 28.801
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 2.2M Sodium chloride, 0.1M BIS-TRIS propane pH 7.0
Matthews coefficient: 3.39
Solvent content (%): 63.7
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: 2018-01-24
Ternary complex of human DNA polymerase eta inserting rCTP opposite template G (PDB entry 5EWE)
Macromolecule: DNA polymerase eta
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.7.7
Sequence length: 435 residues
Sequence: GPHMATGQDRVVALVDMDCFFVQVEQRQNPHLRNKPCAVVQYKSWKGGGIIAVSYEARAFGVTRSMWADDAKKLCPDLLLAQVRESRGKANLTKYREASVEVMEIMSRFAVIERASIDEAYVDLTSAVQERLQKLQGQPISADLLPSTYIEGLPQGPTTAEETVQKEGMRKQGLFQWLDSLQIDNLTSPDLQLTVGAVIVEEMRAAIERETGFQCSAGISHNKVLAKLACGLNKPNRQTLVSHGSVPQLFSQMPIRKIRSLGGKLGASVIEILGIEYMGELTQFTESQLQSHFGEKNGSWLYAMCRGIEHDPVKPRQLPKTIGCSKNFPGKTALATREQVQWWLLQLAQELEERLTKDRNDNDRVATQLVVSIRVQGDKRLSSLRRCCALTRYDAHKMSHDAFTVIKNCNTSGIQTEWSPPLTMLFLCATKFSAS
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.66
R work: 0.1714
R free: 0.2074
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6
Crystallization temperature (K): 291
Crystal growth procedure: NaMES (pH 6.0), polyethylene glycol monomethyl ether 2000, and calcium chloride
Matthews coefficient: 2.13
Solvent content (%): 42.25
Ligand: CYTIDINE-5'-TRIPHOSPHATE (CTP)
Ligand formula: C9 H16 N3 O14 P3
Ligand molecular weight: 483.156
Ligand SMILES: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O
Ligand InChI: InChI=1S/C9H16N3O14P3/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(24-8)3-23-28(19,20)26-29(21,22)25-27(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,21,22)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
Release date: 2016-01-13
The PDZ domain of SNTG1 complexed with the phosphomimetic mutant PDZ-binding motif of RSK1 (PDB entry 7PC8)
Macromolecule: Gamma-1-syntrophin,Annexin A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 414 residues
Sequence: GSHMGGERTVTIRRQTVGGFGLSIKGGAEHNIPVVVSKISKEQRAELSGLLFIGDAILQINGINVRKCRHEEVVQVLRNAGEEVTLTVSFLKRAPGSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2023
R free: 0.2318
Average B factor: 61.7162
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.15 M Lithium sulfate, 0.05 M Magnesium chloride hexahydrate ,0.1 M HEPES 7.8, 20 % v/v PEG Smear High
Matthews coefficient: 3.96
Solvent content (%): 68.97
Ligand: CALCIUM ION (CA)
Ligand formula: Ca
Ligand molecular weight: 40.078
Ligand SMILES: [Ca+2]
Ligand InChI: InChI=1S/Ca/q+2
Release date: 2022-04-20
Human PIM1 bound to benzothiophene inhibitor 224 (PDB entry 6PDI)
Macromolecule: Serine/threonine-protein kinase pim-1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 313 residues
Sequence: SMLLSKINSLAHLRAAPCNDLHATKLAPGKEKEPLESQYQVGPLLGSGGFGSVYSGIRVSDNLPVAIKHVEKDRISDWGELPNGTRVPMEVVLLKKVSSGFSGVIRLLDWFERPDSFVLILERPEPVQDLFDFITERGALQEELARSFFWQVLEAVRHCHNCGVLHRDIKDENILIDLNRGELKLIDFGSGALLKDTVYTDFDGTRVYSPPEWIRYHRYHGRSAAVWSLGILLYDMVCGDIPFEHDEEIIGGQVFFRQRVSSECQHLIRWCLALRPSDRPTFEEIQNHPWMQDVLLPQETAEIHLHSLSPGPS
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.85
R work: 0.1614
R free: 0.1931
Average B factor: 53.452
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG6000, 0.1M TRIS pH7.5, 0.1M magnesium chloride, 10% ethylene glycol
Matthews coefficient: 2.92
Solvent content (%): 57.9
Ligand: 4-(5-{[(3-aminophenyl)methyl]carbamoyl}thiophen-2-yl)-1-benzothiophene-2-carboxamide (OCJ)
Ligand formula: C21 H17 N3 O2 S2
Ligand molecular weight: 407.509
Ligand SMILES: c1cc(cc(c1)N)CNC(=O)c2ccc(s2)c3cccc4c3cc(s4)C(=O)N
Ligand InChI: InChI=1S/C21H17N3O2S2/c22-13-4-1-3-12(9-13)11-24-21(26)18-8-7-17(27-18)14-5-2-6-16-15(14)10-19(28-16)20(23)25/h1-10H,11,22H2,(H2,23,25)(H,24,26)
Release date: 2019-07-24
Identification of M4205 a highly selective inhibitor of cKIT mutations for unresectable metastatic or recurrent GIST (PDB entry 7ZW8)
Macromolecule: Mast/stem cell growth factor receptor Kit
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 327 residues
Sequence: PMYEVQWKVVEEINGNNYVYIDPTQLPYDHKWEFPRNRLSFGKTLGAGAFGKVVEATAYGLIKSDAAMTVAVKMLKPSAHLTEREALMSELKVLSYLGNHMNIVNLLGACTIGGPTLVITEYCCYGDLLNFLRRKRDSFICSKTEPAIMEDDELALDLEDLLSFSYQVAKGMAFLASKNCIHRDLAARNILLTHGRITKICDFGLARDIKNDSNYVVKGNARLPVKWMAPESIFNCVYTFESDVWSYGIFLWELFSLGSSPYPGMPVDSKFYKMIKEGFRMLSPEHAPAEMYDIMKTCWDADPLKRPTFKQIVQLIEKQISESTNHI
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.119
R work: 0.2087
R free: 0.2498
Average B factor: 76.56
Crystallization method: VAPOR DIFFUSION
Crystallization pH: 7.25
Crystallization temperature (K): 293
Crystal growth procedure: 9% (w/v) PEG 8K,  0.1 M HEPES
Matthews coefficient: 2.48
Solvent content (%): 50.48
Ligand: ~{N}-[[4-(1-methylpyrazol-4-yl)phenyl]methyl]-6-[7-(3-pyrrolidin-1-ylpropoxy)imidazo[1,2-a]pyridin-3-yl]pyrimidin-4-amine (K3R)
Ligand formula: C29 H32 N8 O
Ligand molecular weight: 508.617
Ligand SMILES: Cn1cc(cn1)c2ccc(cc2)CNc3cc(ncn3)c4cnc5n4ccc(c5)OCCCN6CCCC6
Ligand InChI: InChI=1S/C29H32N8O/c1-35-20-24(18-34-35)23-7-5-22(6-8-23)17-30-28-16-26(32-21-33-28)27-19-31-29-15-25(9-13-37(27)29)38-14-4-12-36-10-2-3-11-36/h5-9,13,15-16,18-21H,2-4,10-12,14,17H2,1H3,(H,30,32,33)
Release date: 2023-02-22
MAGI-1 complexed with a RSK1 peptide (PDB entry 5N7D)
Macromolecule: Membrane-associated guanylate kinase, WW and PDZ domain-containing protein 1,Annexin A2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 427 residues
Sequence: GSMGKPFFTRNPSELKGKFIHTKLRKSSRGFGFTVVGGDEPDEFLQIKSLVLDGPAALDGKMETGDVIVSVNDTCVLGHTHAQVVKIFQSIPIGASVDLELCRGYPLGSSAYGSVKAYTNFDAERDALNIETAIKTKGVDEVTIVNILTNRSNEQRQDIAFAYQRRTKKELASALKSALSGHLETVILGLLKTPAQYDASELKASMKGLGTDEDSLIEIICSRTNQELQEINRVYKEMYKTDLEKDIISDTSGDFRKLMVALAKGRRAEDGSVIDYELIDQDARDLYDAGVKRKGTDVPKWISIMTERSVPHLQKVFDRYKSYSPYDMLESIRKEVKGDLENAFLNLVQCIQNKPLYFADRLYDSMKGKGTRDKVLIRIMVSRSEVDMLKIRSEFKRKYGKSLYYYIQQDTKGDYQKALLYLCGGDD
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.1906
R free: 0.2271
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 5
Crystallization temperature (K): 296
Crystal growth procedure: 8% PEG 400, 100 mM acetate buffer
Matthews coefficient: 3.03
Solvent content (%): 59.44
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: 2017-11-08