Structure of PDB 4wnt Chain A Binding Site BS02

Receptor Information
>4wnt Chain A (length=457) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GKLPPGPLPDFQNTPYCFDQLRRRFGDVFSLQLAWTPVVVLNGLAAVREA
LVTHGEDTADRPPVPITQILGFGPRSQGVFLARYGPAWREQRRFSVSTLR
NLGLGKKSLEQWVTEEAACLCAAFANHSGRPFRPNGLLDKAVSNVIASLT
CGRRFEYDDPRFLRLLDLAQEGLKEESGFLREVLNAVPVLLHIPALAGKV
LRFQKAFLTQLDELLTEHRMTWDPAQPPRDLTEAFLAEMEKAKGNPESSF
NDENLRIVVADLFSAGMVTTSTTLAWGLLLMILHPDVQRRVQQEIDDVIG
QVRRPEMGDQAHMPYTTAVIHEVQRFGDIVPLGVTHMTSRDIEVQGFRIP
KGTTLITNLSSVLKDEAVWEKPFRFHPEHFLDAQGHFVKPEAFLPFSAGR
RACLGEPLARMELFLFFTSLLQHFSFSVPTGQPRPSHHGVFAFLVSPSPY
ELCAVPR
Ligand information
Ligand IDAJN
InChIInChI=1S/C21H24N2O3/c1-12-16-10-23-8-7-14-13-5-3-4-6-18(13)22-20(14)19(23)9-15(16)17(11-26-12)21(24)25-2/h3-6,11-12,15-16,19,22H,7-10H2,1-2H3/t12-,15-,16+,19-/m0/s1
InChIKeyGRTOGORTSDXSFK-XJTZBENFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C(OC)C4=COC(C5CN3CCc1c(nc2ccccc12)C3CC45)C
CACTVS 3.385COC(=O)C1=CO[CH](C)[CH]2CN3CCc4c([nH]c5ccccc45)[CH]3C[CH]12
OpenEye OEToolkits 1.9.2CC1C2CN3CCc4c5ccccc5[nH]c4C3CC2C(=CO1)C(=O)OC
OpenEye OEToolkits 1.9.2C[C@H]1[C@H]2CN3CCc4c5ccccc5[nH]c4[C@@H]3C[C@@H]2C(=CO1)C(=O)OC
CACTVS 3.385COC(=O)C1=CO[C@@H](C)[C@H]2CN3CCc4c([nH]c5ccccc45)[C@@H]3C[C@H]12
FormulaC21 H24 N2 O3
NameAjmalicine;
methyl (19alpha)-19-methyl-16,17-didehydro-18-oxayohimban-16-carboxylate
ChEMBLCHEMBL123325
DrugBankDB15949
ZINCZINC000053147422
PDB chain4wnt 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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PDB4wnt Contributions of Ionic Interactions and Protein Dynamics to Cytochrome P450 2D6 (CYP2D6) Substrate and Inhibitor Binding.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		L110 F120 A209 L213 E216 Q244 F247 D301 S304 A305 F483
Binding residue
(residue number reindexed from 1)		L70 F80 A169 L173 E176 Q204 F207 D261 S264 A265 F443
Annotation score1
Binding affinityBindingDB: Ki=4.6nM
Enzymatic activity
Catalytic site (original residue number in PDB) T309 F436 C443
Catalytic site (residue number reindexed from 1) T269 F396 C403
Enzyme Commision number 1.14.14.-
Gene Ontology
Molecular Function
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
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:0020037 heme binding
GO:0046872 metal ion binding
GO:0062187 anandamide 8,9 epoxidase activity
GO:0062188 anandamide 11,12 epoxidase activity
GO:0062189 anandamide 14,15 epoxidase activity
Biological Process
GO:0006631 fatty acid metabolic process
GO:0006805 xenobiotic metabolic process
GO:0008202 steroid metabolic process
GO:0008203 cholesterol metabolic process
GO:0008210 estrogen metabolic process
GO:0009804 coumarin metabolic process
GO:0009820 alkaloid metabolic process
GO:0009822 alkaloid catabolic process
GO:0016098 monoterpenoid metabolic process
GO:0019369 arachidonate metabolic process
GO:0033076 isoquinoline alkaloid metabolic process
GO:0042178 xenobiotic catabolic process
GO:0042572 retinol metabolic process
GO:0042759 long-chain fatty acid biosynthetic process
GO:0051100 negative regulation of binding
GO:0070989 oxidative demethylation
GO:0090350 negative regulation of cellular organofluorine metabolic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005783 endoplasmic reticulum
GO:0005789 endoplasmic reticulum membrane
GO:0016020 membrane
GO:0043231 intracellular membrane-bounded organelle

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Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4wnt, PDBe:4wnt, PDBj:4wnt
PDBsum4wnt
PubMed25555909
UniProtP10635|CP2D6_HUMAN Cytochrome P450 2D6 (Gene Name=CYP2D6)

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