satarupa22/MacromolecularLigandDB huggingface dataset:
Human Cytochrome P450 17A1 in complex with steroidal isonitrile inhibitor (PDB entry 8FDA)
Macromolecule: Steroid 17-alpha-hydroxylase/17,20 lyase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.19
Sequence length: 494 residues
Sequence: MAKKTGAKYPKSLLSLPLVGSLPFLPRHGHMHNNFFKLQKKYGPIYSVRMGTKTTVIVGHHQLAKEVLIKKGKDFSGRPQMATLDIASNNRKGIAFADSGAHWQLHRRLAMATFALFKDGDQKLEKIICQEISTLCDMLATHNGQSIDISFPVFVAVTNVISLICFNTSYKNGDPELNVIQNYNEGIIDNLSKDSLVDLVPWLKIFPNKTLEKLKSHVKIRNDLLNKILENYKEKFRSDSITNMLDTLMQAKMNSDNGNAGPDQDSELLSDNHILTTIGDIFGAGVETTTSVVKWTLAFLLHNPQVKKKLYEEIDQNVGFSRTPTISDRNRLLLLEATIREVLRLRPVAPMLIPHKANVDSSIGEFAVDKGTEVIINLWALHHNEKEWHQPDQFMPERFLNPAGTQLISPSVSYLPFGAGPRSCIGEILARQELFLIMAWLLQRFDLEVPDDGQLPSLEGIPKVVFLIDSFKVKIKVRQAWREAQAEGSTHHHH
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.2
R work: 0.2158
R free: 0.2594
Average B factor: 55.7
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 295
Crystal growth procedure: 0.1 M Tris-HCl (pH 8.5), 0.25 M LiSO4, 30% PEG 3350, and 7% sucrose
Matthews coefficient: 2.52
Solvent content (%): 51.27
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: 2023-08-23
Soluble epoxide hydrolase in complex with RK4 (PDB entry 8QMZ)
Macromolecule: Bifunctional epoxide hydrolase 2
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.3.2.10
Sequence length: 367 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMLNTPAPLPTSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDARNPPVVSKMLLEHHHHHH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.47
R work: 0.18752
R free: 0.21408
Average B factor: 21.377
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7
Crystallization temperature (K): 293
Crystal growth procedure: 20% PEG6000, 10% ethylene glycol, 0.1M HEPES pH 7.0, 0.1M calcium chloride
Matthews coefficient: 2.04
Solvent content (%): 39.79
Ligand: (3~{a}~{R},6~{a}~{S})-~{N}-[(2,4-dichlorophenyl)methyl]-2-(4-methylphenyl)sulfonyl-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-5-carboxamide (W6O)
Ligand formula: C22 H24 Cl2 N2 O3 S
Ligand molecular weight: 467.409
Ligand SMILES: Cc1ccc(cc1)S(=O)(=O)N2CC3CC(CC3C2)C(=O)NCc4ccc(cc4Cl)Cl
Ligand InChI: InChI=1S/C22H24Cl2N2O3S/c1-14-2-6-20(7-3-14)30(28,29)26-12-17-8-16(9-18(17)13-26)22(27)25-11-15-4-5-19(23)10-21(15)24/h2-7,10,16-18H,8-9,11-13H2,1H3,(H,25,27)/t16-,17+,18-
Release date: 2024-02-14
novel orally efficacious inhibitors complexed with PARP1 (PDB entry 5XSR)
Macromolecule: Poly [ADP-ribose] polymerase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.4.2.30
Sequence length: 355 residues
Sequence: GPLGSKSKLPKPVQDLIKMIFDVESMKKAMVEYEIDLQKMPLGKLSKRQIQAAYSILSEVQQAVSQGSSDSQILDLSNRFYTLIPHDFGMKKPPLLNNADSVQAKAEMLDNLLDIEVAYSLLRGGSDDSSKDPIDVNYEKLKTDIKVVDRDSEEAEIIRKYVKNTHATTHNAYDLEVIDIFKIEREGECQRYKPFKQLHNRRLLWHGSRTTNFAGILSQGLRIAPPEAPVTGYMFGKGIYFADMVSKSANYCHTSQGDPIGLILLGEVALGNMYELKHASHISKLPKGKHSVKGLGKTTPDPSANISLDGVDVPLGTGISSGVNDTSLLYNEYIVYDIAQVNLKYLLKLKFNFKT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.3
R work: 0.2128
R free: 0.2334
Average B factor: 47.0058
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 80mM NaCl, 1.9M (NH4)2SO4
Matthews coefficient: 3.64
Solvent content (%): 66.19
Ligand: 6-fluoranyl-2-(4,5,6,7-tetrahydrothieno[2,3-c]pyridin-2-yl)-1~{H}-benzimidazole-4-carboxamide (8EC)
Ligand formula: C15 H13 F N4 O S
Ligand molecular weight: 316.353
Ligand SMILES: c1c(cc2c(c1C(=O)N)nc([nH]2)c3cc4c(s3)CNCC4)F
Ligand InChI: InChI=1S/C15H13FN4OS/c16-8-4-9(14(17)21)13-10(5-8)19-15(20-13)11-3-7-1-2-18-6-12(7)22-11/h3-5,18H,1-2,6H2,(H2,17,21)(H,19,20)
Release date: 2018-04-25
Crystal Structure of human Focal Adhesion Targeting (FAT) domain of the Focal Adhesion Kinase (PDB entry 7W7Z)
Macromolecule: Isoform 5 of Focal adhesion kinase 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 164 residues
Sequence: SSPADSYNEGVKPWRLQPQEISPPPTANLDRSNDKVYENVTGLVKAVIEMSSKIQPAPPEEYVPMVKEVGLALRTLLATVDETIPLLPASTHREIEMAQKLLNSDLGELINKMKLAQQYVMTSLQQEYKKQMLTAAHALAVDAKNLLDVIDQARLKMLGQTRPH
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.15
R work: 0.1952
R free: 0.2392
Average B factor: 69.639
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293
Crystal growth procedure: 1.0 M Lithium sulfate 0.1 M MES pH 6.5
Matthews coefficient: 2.17
Solvent content (%): 43.23
Release date: 2022-12-21
CO2 release in human carbonic anhydrase II crystals: reveal histidine 64 and solvent dynamics (PDB entry 5YUK)
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): 1.45
R work: 0.09654
R free: 0.13641
Average B factor: 17.984
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 1.3 M sodium citrate, 100 mM TrisHCl pH 7.8
Matthews coefficient: 2.07
Solvent content (%): 40.69
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: 2018-08-01
Crystal Structure of G12V HRas-GppNHp bound in complex with the engineered RBD variant 1 of CRAF Kinase protein (PDB entry 6NTC)
Macromolecule: GTPase HRas
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 171 residues
Sequence: GAMDPMTEYKLVVVGAVGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQH
Oligomeric state: Hetero 2-mer
Stoichiometry: A1, B1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.9
R work: 0.2517
R free: 0.2781
Average B factor: 145.1335
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 293.15
Crystal growth procedure: 30% PEG4000, 200mM NH4SO4, 100mM Na CaCo pH 6.5
Matthews coefficient: 3.46
Solvent content (%): 64.4
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: 2020-03-04
KRas G12C in complex with G-2897 (PDB entry 7MDP)
Macromolecule: IgG heavy chain
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 226 residues
Sequence: EVQLQESGPGLVKPPGTLSLTCAVSGGSISSSNWWSWVRQPPGKGLEWIGEIYHSGSTNYNPSLKSRVTISVDKSKNQFSLKLSSVTAADTAVYYCARGSSSWYDLGPFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPKSCD
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.96
R work: 0.1948
R free: 0.2288
Average B factor: 57.5263
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 292
Crystal growth procedure: 0.1 M MES pH 6.0, 21 % PEG 4K and 0.2 M lithium sulfate
Matthews coefficient: 3.57
Solvent content (%): 65.56
Ligand: 4-(trifluoromethyl)-1,3-benzothiazol-2-amine (Z07)
Ligand formula: C8 H5 F3 N2 S
Ligand molecular weight: 218.199
Ligand SMILES: c1cc(c2c(c1)sc(n2)N)C(F)(F)F
Ligand InChI: InChI=1S/C8H5F3N2S/c9-8(10,11)4-2-1-3-5-6(4)13-7(12)14-5/h1-3H,(H2,12,13)
Release date: 2022-03-16
The atomic structure of SHP2 E76A mutant in complex with allosteric inhibitor 9b (PDB entry 5XZR)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 11
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 557 residues
Sequence: MGSSHHHHHHSSGLVPRGSHMASMTSRRWFHPNITGVEAENLLLTRGVDGSFLARPSKSNPGDFTLSVRRNGAVTHIKIQNTGDYYDLYGGEKFATLAALVQYYMEHHGQLKEKNGDVIELKYPLNCADPTSERWFHGHLSGKEAEKLLTEKGKHGSFLVRESQSHPGDFVLSVRTGDDKGESNDGKSKVTHVMIRCQELKYDVGGGERFDSLTDLVEHYKKNPMVETLGTVLQLKQPLNTTRINAAEIESRVRELSKLAETTDKVKQGFWEEFETLQQQECKLLYSRKEGQRQENKNKNRYKNILPFDHTRVVLHDGDPNEPVSDYINANIIMPEFETKCNNSKPKKSYIATQGCLQNTVNDFWRMVFQENSRVIVMTTKEVERGKSKCVKYWPDEYALKEYGVMRVRNVKESAAHDYTLRELKLSKVGQGNTERTVWQYHFRTWPDHGVPSDPGGVLDFLEEVHHKQESIMDAGPVVVHCSAGIGRTGTFIVIDILIDIIREKGVDCDIDVPKTIQMVRSQRSGMVQTEAQYRFIYMAVQHYIETLQRRIEEEQK
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.8
R work: 0.2404
R free: 0.2809
Average B factor: 61.1661
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 8.5
Crystallization temperature (K): 291
Crystal growth procedure: 0.2 M Sodium formate, 0.1 M Bicine pH 8.5, 15% w/v PEG 5000MME
Matthews coefficient: 2.11
Solvent content (%): 37.72
Ligand: 4-(3-phenylphenyl)-N-(2,2,6,6-tetramethylpiperidin-4-yl)-1,3-thiazol-2-amine (8J6)
Ligand formula: C24 H29 N3 S
Ligand molecular weight: 391.572
Ligand SMILES: CC1(CC(CC(N1)(C)C)Nc2nc(cs2)c3cccc(c3)c4ccccc4)C
Ligand InChI: InChI=1S/C24H29N3S/c1-23(2)14-20(15-24(3,4)27-23)25-22-26-21(16-28-22)19-12-8-11-18(13-19)17-9-6-5-7-10-17/h5-13,16,20,27H,14-15H2,1-4H3,(H,25,26)
Release date: 2017-12-13
Ternary DNA Polymerase Beta bound to DNA containing primer terminal dA base-paired with FapydG (PDB entry 8VFB)
Macromolecule: DNA (5'-D(*CP*CP*GP*AP*CP*CP*(FAP)P*CP*GP*CP*AP*TP*CP*AP*GP*C)-3')
Type: DNA, polydeoxyribonucleotide
Source organism: synthetic construct
Sequence length: 16 residues
Sequence: CCGACCXCGCATCAGC
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.64
R work: 0.1955
R free: 0.2275
Average B factor: 33.3
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 291
Crystal growth procedure: 14-22% PEG 3350
0.05 M Imidazole pH 8.0
0.35 M Sodium Acetate
Matthews coefficient: 2.39
Solvent content (%): 48.62
Ligand: PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER (G2P)
Ligand formula: C11 H18 N5 O13 P3
Ligand molecular weight: 521.208
Ligand SMILES: c1nc2c(n1C3C(C(C(O3)COP(=O)(CP(=O)(O)OP(=O)(O)O)O)O)O)N=C(NC2=O)N
Ligand InChI: InChI=1S/C11H18N5O13P3/c12-11-14-8-5(9(19)15-11)13-2-16(8)10-7(18)6(17)4(28-10)1-27-30(20,21)3-31(22,23)29-32(24,25)26/h2,4,6-7,10,17-18H,1,3H2,(H,20,21)(H,22,23)(H2,24,25,26)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1
Release date: 2024-05-08
PanDDA Analysis group deposition -- Crystal structure of PTP1B in complex with FMOPL000729a (PDB entry 7GSC)
Macromolecule: Tyrosine-protein phosphatase non-receptor type 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 3.1.3.48
Sequence length: 321 residues
Sequence: MEMEKEFEQIDKSGSWAAIYQDIRHEASDFPSRVAKLPKNKNRNRYRDVSPFDHSRIKLHQEDNDYINASLIKMEEAQRSYILTQGPLPNTVGHFWEMVWEQKSRGVVMLNRVMEKGSLKCAQYWPQKEEKEMIFEDTNLKLTLISEDIKSYYTVRQLELENLTTQETREILHFHYTTWPDFGVPESPASFLNFLFKVRESGSLSPEHGPVVVHCSAGIGRSGTFCLADTCLLLMDKRKDPSSVDIKKVLLEMRKFRMGLIQTADQLRFSYLAVIEGAKFIMGDSSVQDQWKELSHEDLEPPPEHIPPPPRPPKRILEPHN
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.69
R work: 0.1929
R free: 0.2276
Average B factor: 35.604
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization pH: 7.5
Crystallization temperature (K): 277
Crystal growth procedure: 0.3 M magnesium acetate, 0.1 M HEPES pH 7.5, 0.1% beta-mercaptoethanol, 13-14% PEG 8000, 2% ethanol
Matthews coefficient: 3.3
Solvent content (%): 62.74
Ligand: (azepan-1-yl)(2,6-difluorophenyl)methanone (WLJ)
Ligand formula: C13 H15 F2 N O
Ligand molecular weight: 239.261
Ligand SMILES: c1cc(c(c(c1)F)C(=O)N2CCCCCC2)F
Ligand InChI: InChI=1S/C13H15F2NO/c14-10-6-5-7-11(15)12(10)13(17)16-8-3-1-2-4-9-16/h5-7H,1-4,8-9H2
Release date: 2024-01-24
Structure of a human 4E-T - DDX6 - CNOT1 complex (PDB entry 5ANR)
Macromolecule: CCR4-NOT TRANSCRIPTION COMPLEX SUBUNIT 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
Sequence length: 258 residues
Sequence: QGPDSMKKDVPPSINTTNIDTLLVATDQTERIVEPPENIQEKIAFIFNNLSQSNMTQKVEELKETVKEEFMPWVSQYLVMKRVSIEPNFHSLYSNFLDTLKNPEFNKMVLNETYRNIKVLLTSDKAAANFSDRSLLKNLGHWLGMITLAKNKPILHTDLDVKSLLLEAYVKGQQELLYVVPFVAKVLESSIRSVVFRPPNPWTMAIMNVLAELHQEHDLKLNLKFEIEVLCKNLALDINELKPGNLLKDKDRLKNLDE
Oligomeric state: Hetero 3-mer
Stoichiometry: A1, B1, C1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.102
R work: 0.1931
R free: 0.2319
Crystallization pH: 8
Crystal growth procedure: 50 MM TRIS PH 8.0, 35% MPD
Matthews coefficient: 2.32
Solvent content (%): 47.01
Release date: 2015-10-21
HUMAN JAK3 IN COMPLEX WITH LASW959 PROTEIN IN COMPLEX WITH LIGAND (PDB entry 6HZV)
Macromolecule: Tyrosine-protein kinase JAK3
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.2
Sequence length: 285 residues
Sequence: TIFEERHLKYISQLGKGNFGSVELCRYDPLGDNTGALVAVKQLQHSGPDQQRDFQREIQILKALHSDFIVKYRGVSYGPGRQSLRLVMEYLPSGCLRDFLQRHRARLDASRLLLYSSQICKGMEYLGSRRCVHRDLAARNILVESEAHVKIADFGLAKLLPLDKDYYVVREPGQSPIFWYAPESLSDNIFSRQSDVWSFGVVLYELFTYCDKSCSPSAEFLRMMGCERDVPALSRLLELLEEGQRLPAPPACPAEVHELMKLCWAPSPQDRPSFSALGPQLDMLW
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.46
R work: 0.22278
R free: 0.27533
Average B factor: 37.51
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 277
Crystal growth procedure: 30% PEG3350, 0.1M BIS-TRIS, 0.2M MgCl, pH 6.0
Matthews coefficient: 2.52
Solvent content (%): 51.3
Ligand: 3-[7-(2-hydroxyethyl)-9-(oxan-4-yl)-8-oxidanylidene-purin-2-yl]imidazo[1,2-a]pyridine-6-carbonitrile (GYW)
Ligand formula: C20 H19 N7 O3
Ligand molecular weight: 405.41
Ligand SMILES: c1cc2ncc(n2cc1C#N)c3ncc4c(n3)N(C(=O)N4CCO)C5CCOCC5
Ligand InChI: InChI=1S/C20H19N7O3/c21-9-13-1-2-17-22-10-15(26(17)12-13)18-23-11-16-19(24-18)27(14-3-7-30-8-4-14)20(29)25(16)5-6-28/h1-2,10-12,14,28H,3-8H2
Release date: 2019-10-23
Structure of human galactokinase 1 bound with 2-(4-chlorophenyl)-N-(pyrimidin-2-yl)acetamide (PDB entry 6ZH0)
Macromolecule: Galactokinase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.1.6
Sequence length: 399 residues
Sequence: MAHHHHHHAALRQPQVAELLAEARRAFREEFGAEPELAVSAPGRVNLIGEHTDYNQGLVLPMALELMTVLVGSPRKDGLVSLLTTSEGADEPQRLQFPLPTAQRSLEPGTPRWANYVKGVIQYYPAAPLPGFSAVVVSSVPLGGGLSSSASLEVATYTFLQQLCPDSGTIAARAQVCQQAEHSFAGMPCGIMDQFISLMGQKGHALLIDCRSLETSLVPLSDPKLAVLITNSNVRHSLASSEYPVRRRQCEEVARALGAASLREVQLEELEAARDLVSKEGFRRARHVVGEIRRTAQAAAALRRGDYRAFGRLMVESHRSLRDDYEVSCPELDQLVEAALAVPGVYGSRMTGGGFGGCTVTLLEASAAPHAMRHIQEHYGGTATFYLSQAADGAKVLCL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.5
R work: 0.2389
R free: 0.2897
Average B factor: 50.803
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M MOPS/sodium HEPES pH 7.0-7.5, 40-50 % Morpheus Precipitant Mix 4 (50% mix = 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350), 0.1 M Morpheus Carboxylic acids mix (0.02M each of - sodium formate, ammonium acetate, sodium citrate tribasic dehydrate, sodium potassium tartrate tetrahydrate and sodium oxamate).
Matthews coefficient: 2.91
Solvent content (%): 57.77
Ligand: N-(3-chlorophenyl)-2,2,2-trifluoroacetamide (WNP)
Ligand formula: C8 H5 Cl F3 N O
Ligand molecular weight: 223.58
Ligand SMILES: c1cc(cc(c1)Cl)NC(=O)C(F)(F)F
Ligand InChI: InChI=1S/C8H5ClF3NO/c9-5-2-1-3-6(4-5)13-7(14)8(10,11)12/h1-4H,(H,13,14)
Release date: 2022-06-01
Human CYP3A4 bound to an inhibitor (PDB entry 7KVO)
Macromolecule: Cytochrome P450 3A4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 1.14.14.1
Sequence length: 487 residues
Sequence: MAYLYGTHSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDGQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWKRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFGAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFPFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTQKHRVDFLQLMIDSQNSKETESHKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVESRDGTVSGAHHHH
Oligomeric state: Homo 2-mer
Stoichiometry: A2
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.65
R work: 0.241
R free: 0.2928
Crystallization method: MICROBATCH
Crystallization pH: 7
Crystallization temperature (K): 298
Crystal growth procedure: PEG 3350, sodium succinate
Matthews coefficient: 2.59
Solvent content (%): 52.43
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: 2021-01-20
Crystal structure of MYST acetyltransferase domain in complex with inhibitor 83 (PDB entry 6PDG)
Macromolecule: Histone acetyltransferase KAT8
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.3.1.48
Sequence length: 272 residues
Sequence: KYVDKIHIGNYEIDAWYFSPFPEDYGKQPKLWLCEYCLKYMKYEKSYRFHLGQCQWRQPPGKEIYRKSNISVHEVDGKDHKIYCQNLCLLAKLFLDHKTLYFDVEPFVFYILTEVDRQGAHIVGYFSKEKESPDGNNVSCIMILPPYQRRGYGRFLIAFSYELSKLESTVGSPEKPLSDLGKLSYRSYWSSVLLENLRDFRGTLSIKDLSQMTSITQNDIISTLQSLNMVKYWKGQHVICVTPKLVEEHLKSAQYKKPPITVDSVCLKWAPP
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.919
R work: 0.1912
R free: 0.2131
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.5
Crystallization temperature (K): 292
Crystal growth procedure: 27% PEG 3350, 0.2 M ammonium sulfate, 0.1 M bis-tris pH 6.5
Matthews coefficient: 2.5
Solvent content (%): 50.87
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: 2020-04-01
IRAK4 IN COMPLEX WITH inhibitor (PDB entry 6F3E)
Macromolecule: Interleukin-1 receptor-associated kinase 4
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.11.1
Sequence length: 295 residues
Sequence: RFHSFSFYELKNVTNNFDERPISVGGNKMGEGGFGVVYKGYVNNTTVAVKKLAAMVDITTEELKQQFDQEIKVMAKCQHENLVELLGFSSDGDDLCLVYVYMPNGSLLDRLSCLDGTPPLSWHMRCKIAQGAANGINFLHENHHIHRDIKSANILLDEAFTAKISDFGLARASEKFAQTVMTSRIVGTTAYMAPEALRGEITPKSDIYSFGVVLLEIITGLPAVDEHREPQLLLDIKEEIEDEEKTIEDYIDKKMNDADSTSVEAMYSVASQCLHEKKNKRPDIKKVQQLLQEMT
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.67
R work: 0.1985
R free: 0.2544
Average B factor: 85.09
Crystallization method: VAPOR DIFFUSION
Crystallization temperature (K): 293
Crystal growth procedure: 50 mM Hepes pH 7.5, 0.02% octylglucoside, 10% glycerol, 0.3 M NaCl, 1 mM TCEP
Matthews coefficient: 2.56
Solvent content (%): 51.95
Ligand: 2-[(3~{R})-12-(4-morpholin-4-ylcyclohexyl)oxy-7-thia-9,11-diazatricyclo[6.4.0.0^{2,6}]dodeca-1(8),2(6),9,11-tetraen-3-yl]ethanamide (CJQ)
Ligand formula: C21 H28 N4 O3 S
Ligand molecular weight: 416.537
Ligand SMILES: c1nc(c2c3c(sc2n1)CCC3CC(=O)N)OC4CCC(CC4)N5CCOCC5
Ligand InChI: InChI=1S/C21H28N4O3S/c22-17(26)11-13-1-6-16-18(13)19-20(23-12-24-21(19)29-16)28-15-4-2-14(3-5-15)25-7-9-27-10-8-25/h12-15H,1-11H2,(H2,22,26)/t13-,14-,15-/m1/s1
Release date: 2018-05-23
Crystal structure of FGFR1 (C488A, C584C) in complex with 6-(7-((1-aminocyclopropyl) methoxy)-6-methoxyquinolin-4-yloxy)-N-methyl-1-naphthamide (E3810) (PDB entry 4RWL)
Macromolecule: Fibroblast growth factor receptor 1
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.7.10.1
Sequence length: 317 residues
Sequence: MGHHHHHHMAGVSEYELPEDPRWELPRDRLVLGKPLGEGAFGQVVLAEAIGLDKDKPNRVTKVAVKMLKSDATEKDLSDLISEMEMMKMIGKHKNIINLLGACTQDGPLYVIVEYASKGNLREYLQARRPPGLEYSYNPSHNPEEQLSSKDLVSCAYQVARGMEYLASKKCIHRDLAARNVLVTEDNVMKIADFGLARDIHHIDYYKKTTNGRLPVKWMAPEALFDRIYTHQSDVWSFGVLLWEIFTLGGSPYPGVPVEELFKLLKEGHRMDKPSNCTNELYMMMRDCWHAVPSQRPTFKQLVEDLDRIVALTSNQE
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 2.193
R work: 0.2068
R free: 0.2555
Average B factor: 47.8932
Crystallization method: VAPOR DIFFUSION, HANGING DROP
Crystallization pH: 6.6
Crystallization temperature (K): 293
Crystal growth procedure: 0.1 M sodium cacodylate pH 6.6, 34% PEG 8000, 0.2 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Matthews coefficient: 2.59
Solvent content (%): 52.59
Ligand: 6-({7-[(1-aminocyclopropyl)methoxy]-6-methoxyquinolin-4-yl}oxy)-N-methylnaphthalene-1-carboxamide (3ZC)
Ligand formula: C26 H25 N3 O4
Ligand molecular weight: 443.494
Ligand SMILES: CNC(=O)c1cccc2c1ccc(c2)Oc3ccnc4c3cc(c(c4)OCC5(CC5)N)OC
Ligand InChI: InChI=1S/C26H25N3O4/c1-28-25(30)19-5-3-4-16-12-17(6-7-18(16)19)33-22-8-11-29-21-14-24(23(31-2)13-20(21)22)32-15-26(27)9-10-26/h3-8,11-14H,9-10,15,27H2,1-2H3,(H,28,30)
Release date: 2015-04-15
Crystal structure of small molecule 13 bound to human Nicotinamide N-methyltransferase (PDB entry 7WMT)
Macromolecule: Nicotinamide N-methyltransferase
Type: Protein, polypeptide(L)
Source organism: Homo sapiens
EC number: 2.1.1.1
Sequence length: 250 residues
Sequence: GSGFTSKDTYLSHFNPRDYLEKYYKFGSRHSAESQILKHLLKNLFKIFCLDGVKGDLLIDIGSGPTIYQLLSACESFKEIVVTDYSDQNLQELEKWLKKEPAAFDWSPVVTYVCDLEGNRVKGPEKEEKLRQAVKQVLKCDVTQSQPLGAVPLPPADCVLSTLCLDAACPDLPTYCRALRNLGSLLKPGGFLVIMDALKGGGGREAVEAAVKEAGYTIEWFEVISQSYSSTMANNEGLFSLVARKLSRPL
Oligomeric state: Monomer
Stoichiometry: A1
Experimental method: X-RAY DIFFRACTION
Refinement resolution (Å): 1.77
R work: 0.1548
R free: 0.1909
Average B factor: 43.953
Crystallization method: VAPOR DIFFUSION, SITTING DROP
Crystallization temperature (K): 277
Crystal growth procedure: 0.04 M Potassium phosphate monobasic, 16 % w/v PEG 8000, 20 % v/v Glycerol
Matthews coefficient: 2.75
Solvent content (%): 55.23
Ligand: [(2~{R},4~{S})-4-[2-(aminomethyl)imidazol-1-yl]-2-[1-[(4-chlorophenyl)methyl]-5-methyl-indol-2-yl]pyrrolidin-1-yl]-(1~{H}-pyrrolo[2,3-b]pyridin-5-yl)methanone (1IV)
Ligand formula: C32 H30 Cl N7 O
Ligand molecular weight: 564.08
Ligand SMILES: Cc1ccc2c(c1)cc(n2Cc3ccc(cc3)Cl)C4CC(CN4C(=O)c5cc6cc[nH]c6nc5)n7ccnc7CN
Ligand InChI: InChI=1S/C32H30ClN7O/c1-20-2-7-27-23(12-20)14-28(39(27)18-21-3-5-25(33)6-4-21)29-15-26(38-11-10-35-30(38)16-34)19-40(29)32(41)24-13-22-8-9-36-31(22)37-17-24/h2-14,17,26,29H,15-16,18-19,34H2,1H3,(H,36,37)/t26-,29+/m0/s1
Release date: 2022-08-31