Structure of PDB 4d75 Chain A Binding Site BS01

Receptor Information
>4d75 Chain A (length=460) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
HSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYDG
QQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEWK
RLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVFG
AYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLLRFDFLDPFFLSITVFP
FLIPILEVLNICVFPREVTNFLRKSVKRMKESRLEHRVDFLQLMIDSQNS
HKALSDLELVAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEID
AVLPNKAPPTYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGM
FIPKGVVVMIPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFG
SGPRNCIGMRFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPE
KPVVLKVESR
Ligand information
Ligand IDPK9
InChIInChI=1S/C17H27N3O3/c1-17(2,3)23-16(22)19-11-6-4-5-9-15(21)20-13-14-8-7-10-18-12-14/h7-8,10,12H,4-6,9,11,13H2,1-3H3,(H,19,22)(H,20,21)
InChIKeyLDXDSDSWWMTDPA-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 1.7.6		CC(C)(C)OC(=O)NCCCCCC(=O)NCc1cccnc1
ACDLabs 12.01O=C(OC(C)(C)C)NCCCCCC(=O)NCc1cccnc1
FormulaC17 H27 N3 O3
Nametert-butyl {6-oxo-6-[(pyridin-3-ylmethyl)amino]hexyl}carbamate
ChEMBLCHEMBL3814075
DrugBank
ZINCZINC000121986305
PDB chain4d75 Chain A Residue 600 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4d75 Structure-Based Inhibitor Design for Evaluation of a Cyp3A4 Pharmacophore Model.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		S119 R212 I301 F304 A305 T309
Binding residue
(residue number reindexed from 1)		S92 R185 I265 F268 A269 T273
Annotation score1
Binding affinityMOAD: Kd=105uM
BindingDB: Kd=105000nM,IC50=75000nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4d75, PDBe:4d75, PDBj:4d75
PDBsum4d75
PubMed26371436
UniProtP08684|CP3A4_HUMAN Cytochrome P450 3A4 (Gene Name=CYP3A4)

[Back to BioLiP]