Structure of PDB 6bdk Chain A Binding Site BS02

Receptor Information
>6bdk Chain A (length=461) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
THSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYD
GQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEW
KRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVF
GAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVF
PFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDVDFLQLMIDSQNS
HKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEID
AVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGM
FIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFG
SGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPE
KPVVLKVESRD
Ligand information
Ligand IDDJ1
InChIInChI=1S/C30H41N5O3S/c1-30(2,3)38-29(37)35-24(15-22-18-32-26-13-7-6-12-25(22)26)19-39-20-27(34-23-10-4-5-11-23)28(36)33-17-21-9-8-14-31-16-21/h6-9,12-14,16,18,23-24,27,32,34H,4-5,10-11,15,17,19-20H2,1-3H3,(H,33,36)(H,35,37)/t24-,27-/m0/s1
InChIKeyAQDOXNFDADPPBW-IGKIAQTJSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(C)OC(=O)N[C@H](CSC[C@H](NC1CCCC1)C(=O)NCc2cccnc2)Cc3c[nH]c4ccccc34
OpenEye OEToolkits 2.0.6CC(C)(C)OC(=O)NC(Cc1c[nH]c2c1cccc2)CSCC(C(=O)NCc3cccnc3)NC4CCCC4
CACTVS 3.385CC(C)(C)OC(=O)N[CH](CSC[CH](NC1CCCC1)C(=O)NCc2cccnc2)Cc3c[nH]c4ccccc34
OpenEye OEToolkits 2.0.6CC(C)(C)OC(=O)N[C@@H](Cc1c[nH]c2c1cccc2)CSC[C@@H](C(=O)NCc3cccnc3)NC4CCCC4
ACDLabs 12.01C4(NC(C(=O)NCc1cccnc1)CSCC(Cc2cnc3c2cccc3)NC(=O)OC(C)(C)C)CCCC4
FormulaC30 H41 N5 O3 S
Nametert-butyl [(2S)-1-{[(2R)-2-(cyclopentylamino)-3-oxo-3-{[(pyridin-3-yl)methyl]amino}propyl]sulfanyl}-3-(1H-indol-3-yl)propan-2-yl]carbamate
ChEMBL
DrugBank
ZINC
PDB chain6bdk Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6bdk Inhibition of Human CYP3A4 by Rationally Designed Ritonavir-Like Compounds: Impact and Interplay of the Side Group Functionalities.
Resolution2.67 Å
Binding residue
(original residue number in PDB)		R105 F108 S119 R212 F213 F215 F304 A305 T309 I369 A370 R372 E374
Binding residue
(residue number reindexed from 1)		R79 F82 S93 R186 F187 F189 F268 A269 T273 I333 A334 R336 E338
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) T309 F435 C442
Catalytic site (residue number reindexed from 1) T273 F399 C406
Enzyme Commision number 1.14.14.1: unspecific monooxygenase.
1.14.14.55: quinine 3-monooxygenase.
1.14.14.56: 1,8-cineole 2-exo-monooxygenase.
1.14.14.73: albendazole monooxygenase (sufoxide-forming).
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005496 steroid binding
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0008395 steroid hydroxylase activity
GO:0008401 retinoic acid 4-hydroxylase activity
GO:0016491 oxidoreductase activity
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0016712 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen
GO:0019825 oxygen binding
GO:0019899 enzyme binding
GO:0020037 heme binding
GO:0030343 vitamin D3 25-hydroxylase activity
GO:0034875 caffeine oxidase activity
GO:0046872 metal ion binding
GO:0050591 quinine 3-monooxygenase activity
GO:0050649 testosterone 6-beta-hydroxylase activity
GO:0062181 1-alpha,25-dihydroxyvitamin D3 23-hydroxylase activity
GO:0062187 anandamide 8,9 epoxidase activity
GO:0062188 anandamide 11,12 epoxidase activity
GO:0062189 anandamide 14,15 epoxidase activity
GO:0070330 aromatase activity
GO:0070576 vitamin D 24-hydroxylase activity
GO:0101020 estrogen 16-alpha-hydroxylase activity
GO:0101021 estrogen 2-hydroxylase activity
GO:0102320 1,8-cineole 2-exo-monooxygenase activity
Biological Process
GO:0002933 lipid hydroxylation
GO:0006629 lipid metabolic process
GO:0006631 fatty acid metabolic process
GO:0006694 steroid biosynthetic process
GO:0006706 steroid catabolic process
GO:0006805 xenobiotic metabolic process
GO:0008202 steroid metabolic process
GO:0008203 cholesterol metabolic process
GO:0008209 androgen metabolic process
GO:0008210 estrogen metabolic process
GO:0009822 alkaloid catabolic process
GO:0016098 monoterpenoid metabolic process
GO:0036378 calcitriol biosynthetic process from calciol
GO:0042178 xenobiotic catabolic process
GO:0042359 vitamin D metabolic process
GO:0042369 vitamin D catabolic process
GO:0042572 retinol metabolic process
GO:0042573 retinoic acid metabolic process
GO:0042759 long-chain fatty acid biosynthetic process
GO:0046222 aflatoxin metabolic process
GO:0070989 oxidative demethylation
Cellular Component
GO:0005737 cytoplasm
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6bdk, PDBe:6bdk, PDBj:6bdk
PDBsum6bdk
PubMed29232137
UniProtP08684|CP3A4_HUMAN Cytochrome P450 3A4 (Gene Name=CYP3A4)

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