Structure of PDB 8dmg Chain A Binding Site BS02

Receptor Information
>8dmg Chain A (length=1034) Species: 1348623 (Priestia megaterium NBRC 15308 = ATCC 14581) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KEMPQPKTFGELKNLPLLNTDKPVQALMKIADELGEIFKFEAPGRVTRYL
SSQRLIKEACDESRFDKNLSQALKFVRDFFGDGLFTSWTHEKNWKKAHNI
LLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDT
IGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENK
RQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDE
NIRYQIITFLIAGHETTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPV
PSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDE
LMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIG
QQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKK
IPLKKVRKKAENAHNTPLLVLYGSNMGTAEGTARDLADIAMSKGFAPQVA
TLDSHAGNLPREGAVLIVTASYNGHPPDNAKQFVDWLDQASADEVKGVRY
SVFGCGDKNWATTYQKVPAFIDETLAAKGAENIADRGEADASDDFEGTYE
EWREHMWSDVAAYFNLDIENSEDNKSTLSLQFVDSAADMPLAKMHGAFST
NVVASKELQQPGSARSTRHLEIELPKEASYQEGDHLGVIPRNYEGIVNRV
TARFGLDASQQIRLEAEEEKLAHLPLAKTVSVEELLQYVELQDPVTRTQL
RAMAAKTVCPPHKVELEALLEKQAYKEQVLAKRLTMLELLEKYPACEMKF
SEFIALLPSIRPRYYSISSSPRVDEKQASITVSVVSGEAWSGYGEYKGIA
SNYLAELQEGDTITCFISTPQSEFTLPKDPETPLIMVGPGTGVAPFRGFV
QARKQLKEQGQSLGEAHLYFGCRSPHEDYLYQEELENAQSEGIITLHTAF
SRMPNQPKTYVQHVMEQDGKKLIELLDQGAHFYICGDGSQMAPAVEATLM
KSYADVHQVSEADARLWLQQLEEKGRYAKDVWAG
Ligand information
Ligand ID1C6
InChIInChI=1S/C17H19N3O2S/c1-10-8-18-15(11(2)16(10)22-4)9-23-17-19-13-6-5-12(21-3)7-14(13)20-17/h5-8H,9H2,1-4H3,(H,19,20)
InChIKeyXURCIPRUUASYLR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01n2c1ccc(OC)cc1nc2SCc3ncc(c(OC)c3C)C
OpenEye OEToolkits 1.7.6Cc1cnc(c(c1OC)C)CSc2[nH]c3cc(ccc3n2)OC
CACTVS 3.370COc1ccc2nc([nH]c2c1)SCc3ncc(C)c(OC)c3C
FormulaC17 H19 N3 O2 S
Name6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole;
omeprazole;
prilosec
ChEMBLCHEMBL892
DrugBank
ZINCZINC000013603907
PDB chain8dmg Chain A Residue 1102 [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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PDB8dmg Insight into the conformational dynamics of cytochrome P450 CYP102A1 enzyme using Cryo-EM
Resolution4.4 Å
Binding residue
(original residue number in PDB)		F87 L188 A328 P329 L437
Binding residue
(residue number reindexed from 1)		F85 L186 A326 P327 L435
Annotation score1
Enzymatic activity
Enzyme Commision number 1.14.14.1: unspecific monooxygenase.
1.6.2.4: NADPH--hemoprotein reductase.
Gene Ontology
Molecular Function
GO:0003958 NADPH-hemoprotein reductase activity
GO:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0010181 FMN 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:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0050660 flavin adenine dinucleotide binding
GO:0070330 aromatase activity
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Cellular Component
External links
PDB RCSB:8dmg, PDBe:8dmg, PDBj:8dmg
PDBsum8dmg
PubMed
UniProtP14779|CPXB_PRIM2 Bifunctional cytochrome P450/NADPH--P450 reductase (Gene Name=cyp102A1)

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