Structure of PDB 4d78 Chain A Binding Site BS02

Receptor Information
>4d78 Chain A (length=459) 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
PFLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEDTHRVDFLQLMIDS
QALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDA
VLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMF
IPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGS
GPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEK
PVVLKVESR
Ligand information
Ligand IDJ9K
InChIInChI=1S/C23H31N3O3S/c1-23(2,3)29-22(28)26-20(14-18-8-5-4-6-9-18)17-30-13-11-21(27)25-16-19-10-7-12-24-15-19/h4-10,12,15,20H,11,13-14,16-17H2,1-3H3,(H,25,27)(H,26,28)/t20-/m0/s1
InChIKeyMVQZDJDMEHCEJW-FQEVSTJZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CC(C)(C)OC(=O)NC(Cc1ccccc1)CSCCC(=O)NCc2cccnc2
OpenEye OEToolkits 1.7.6CC(C)(C)OC(=O)N[C@@H](Cc1ccccc1)CSCCC(=O)NCc2cccnc2
CACTVS 3.385CC(C)(C)OC(=O)N[CH](CSCCC(=O)NCc1cccnc1)Cc2ccccc2
ACDLabs 12.01O=C(OC(C)(C)C)NC(Cc1ccccc1)CSCCC(=O)NCc2cccnc2
CACTVS 3.385CC(C)(C)OC(=O)N[C@H](CSCCC(=O)NCc1cccnc1)Cc2ccccc2
FormulaC23 H31 N3 O3 S
Nametert-butyl [(2S)-1-({3-oxo-3-[(pyridin-3-ylmethyl)amino]propyl}sulfanyl)-3-phenylpropan-2-yl]carbamate
ChEMBLCHEMBL3814479
DrugBank
ZINCZINC000263620767
PDB chain4d78 Chain A Residue 1600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4d78 Structure-Based Inhibitor Design for Evaluation of a Cyp3A4 Pharmacophore Model.
Resolution2.8 Å
Binding residue
(original residue number in PDB)		F108 L211 I301 F304 A305 I369
Binding residue
(residue number reindexed from 1)		F82 L185 I264 F267 A268 I332
Annotation score1
Binding affinityBindingDB: Kd=900nM,IC50=520nM
Enzymatic activity
Catalytic site (original residue number in PDB) T309 F435 C442
Catalytic site (residue number reindexed from 1) T272 F398 C405
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:4d78, PDBe:4d78, PDBj:4d78
PDBsum4d78
PubMed26371436
UniProtP08684|CP3A4_HUMAN Cytochrome P450 3A4 (Gene Name=CYP3A4)

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