Structure of PDB 7ydd Chain A Binding Site BS04

Receptor Information
>7ydd Chain A (length=454) 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
SSQRLIKEACDESRFDKNLSQALKFIRDFAGDGLATSWTHEKNWKKAHNI
LLPSFSQQAMKGYHAMMVDIAVQLVQKWERLNADEHIEVPEDMTRLTLDT
IGLCGFNYRFNSFYRDQPHPFITSMVRALDEAMNKLQRANPDDPAYDENK
RQFQEDIKVMNDLVDKIIADRKASGEQSDDLLTHMLNGKDPETGEPLDDE
NIRYQIITFLIAGHEPTSGLLSFALYFLVKNPHVLQKAAEEAARVLVDPV
PSYKQVKQLKYVGMVLNEALRLWPTAPAFSLYAKEDTVLGGEYPLEKGDE
LMVLIPQLHRDKTIWGDDVEEFRPERFENPSAIPQHAFKPFGNGQRACIG
QQFALHEATLVLGMMLKHFDFEDHTNYELDIKETLTLKPEGFVVKAKSKK
IPLL
Ligand information
Ligand IDIRV
InChIInChI=1S/C17H21N3O3/c21-16(8-4-5-10-20-11-9-18-13-20)19-15(17(22)23)12-14-6-2-1-3-7-14/h1-3,6-7,9,11,13,15H,4-5,8,10,12H2,(H,19,21)(H,22,23)/t15-/m0/s1
InChIKeyXWFLBNSJOTZCGC-HNNXBMFYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385OC(=O)[CH](Cc1ccccc1)NC(=O)CCCCn2ccnc2
OpenEye OEToolkits 2.0.7c1ccc(cc1)CC(C(=O)O)NC(=O)CCCCn2ccnc2
CACTVS 3.385OC(=O)[C@H](Cc1ccccc1)NC(=O)CCCCn2ccnc2
OpenEye OEToolkits 2.0.7c1ccc(cc1)C[C@@H](C(=O)O)NC(=O)CCCCn2ccnc2
FormulaC17 H21 N3 O3
Name(2~{S})-2-(5-imidazol-1-ylpentanoylamino)-3-phenyl-propanoic acid
ChEMBL
DrugBank
ZINC
PDB chain7ydd Chain A Residue 504 [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]
PDB7ydd Regiodivergent and Enantioselective Hydroxylation of C-H bonds by Synergistic Use of Protein Engineering and Exogenous Dual-Functional Small Molecules.
Resolution1.663 Å
Binding residue
(original residue number in PDB)		L20 F42 R47 Y51 S72 Q73 A74 A328 P329 A330
Binding residue
(residue number reindexed from 1)		L18 F40 R45 Y49 S70 Q71 A72 A326 P327 A328
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:0004497 monooxygenase activity
GO:0005506 iron ion binding
GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0020037 heme binding

View graph for
Molecular Function
External links
PDB RCSB:7ydd, PDBe:7ydd, PDBj:7ydd
PDBsum7ydd
PubMed36417593
UniProtP14779|CPXB_PRIM2 Bifunctional cytochrome P450/NADPH--P450 reductase (Gene Name=cyp102A1)

[Back to BioLiP]