Structure of PDB 6da5 Chain A Binding Site BS02

Receptor Information
>6da5 Chain A (length=451) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
THSHGLFKKLGIPGPTPLPFLGNILSYHKGFCMFDMECHKKYGKVWGFYD
GQQPVLAITDPDMIKTVLVKECYSVFTNRRPFGPVGFMKSAISIAEDEEW
KRLRSLLSPTFTSGKLKEMVPIIAQYGDVLVRNLRREAETGKPVTLKDVF
GAYSMDVITSTSFGVNIDSLNNPQDPFVENTKKLPFFLSITVFPFLIPIL
EVLNICVFPREVTNFLRKSVKRMKESRLVDFLQLMIDSQNSHKALSDLEL
VAQSIIFIFAGYETTSSVLSFIMYELATHPDVQQKLQEEIDAVLPNKAPP
TYDTVLQMEYLDMVVNETLRLFPIAMRLERVCKKDVEINGMFIPKGVVVM
IPSYALHRDPKYWTEPEKFLPERFSKKNKDNIDPYIYTPFGSGPRNCIGM
RFALMNMKLALIRVLQNFSFKPCKETQIPLKLSLGGLLQPEKPVVLKVES
R
Ligand information
Ligand IDG1J
InChIInChI=1S/C29H35N3O3S/c1-29(2,3)35-28(34)32-25(17-22-11-6-4-7-12-22)21-36-26(18-23-13-8-5-9-14-23)27(33)31-20-24-15-10-16-30-19-24/h4-16,19,25-26H,17-18,20-21H2,1-3H3,(H,31,33)(H,32,34)/t25-,26+/m1/s1
InChIKeyDPUYQVBTNSUNNA-FTJBHMTQSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(Cc1ccccc1)(C(=O)NCc2cnccc2)SCC(Cc3ccccc3)NC(=O)OC(C)(C)C
OpenEye OEToolkits 2.0.6CC(C)(C)OC(=O)NC(Cc1ccccc1)CSC(Cc2ccccc2)C(=O)NCc3cccnc3
CACTVS 3.385CC(C)(C)OC(=O)N[CH](CS[CH](Cc1ccccc1)C(=O)NCc2cccnc2)Cc3ccccc3
CACTVS 3.385CC(C)(C)OC(=O)N[C@@H](CS[C@@H](Cc1ccccc1)C(=O)NCc2cccnc2)Cc3ccccc3
OpenEye OEToolkits 2.0.6CC(C)(C)OC(=O)N[C@H](Cc1ccccc1)CS[C@@H](Cc2ccccc2)C(=O)NCc3cccnc3
FormulaC29 H35 N3 O3 S
Nametert-butyl [(2R)-1-{[(2S)-1-oxo-3-phenyl-1-{[(pyridin-3-yl)methyl]amino}propan-2-yl]sulfanyl}-3-phenylpropan-2-yl]carbamate
ChEMBL
DrugBank
ZINC
PDB chain6da5 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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PDB6da5 Structure-Activity Relationships of Rationally Designed Ritonavir Analogues: Impact of Side-Group Stereochemistry, Headgroup Spacing, and Backbone Composition on the Interaction with CYP3A4.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		F108 S119 F241 I301 F304 A305
Binding residue
(residue number reindexed from 1)		F82 S93 F208 I256 F259 A260
Annotation score1
Binding affinityMOAD: Kd=0.07uM
Enzymatic activity
Catalytic site (original residue number in PDB) T309 F435 C442
Catalytic site (residue number reindexed from 1) T264 F390 C397
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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Cellular Component
External links
PDB RCSB:6da5, PDBe:6da5, PDBj:6da5
PDBsum6da5
PubMed30912932
UniProtP08684|CP3A4_HUMAN Cytochrome P450 3A4 (Gene Name=CYP3A4)

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