Structure of PDB 6wkd Chain A Binding Site BS01

Receptor Information
>6wkd Chain A (length=280) Species: 1931 (Streptomyces sp.) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
IPLPGRQSPDHARAEAEQLAWPRSLGLIRSDAAAERHLRGGYADLASRFY
PHATGADLDLGVDLMSWFFLFDDLFDGPRGENPEDTKQLTDQVAAALDGP
LPDTAPPIAHGFADIWRRTCEGMTPAWCARSARHWRNYFDGYVDEAESRF
AAQYLAMRRHTIGVQPTVDLAERAGRFEVPHRVFDSAVMSAMLQIAVDVN
LLLNDIASLNMVMIRSVSHMQNEVRARLEQYLLLESCLPKVGEIYQLDTA
EREALERYRTDAVRTVIRGSYDWHRSSGRY
Ligand information
Ligand IDFDF
InChIInChI=1S/C15H26F2O7P2/c1-13(7-4-8-15(11-16)12-17)5-3-6-14(2)9-10-23-26(21,22)24-25(18,19)20/h5,8-9H,3-4,6-7,10-12H2,1-2H3,(H,21,22)(H2,18,19,20)/b13-5+,14-9+
InChIKeyPVNRGYDHHSWPHV-HJAIQHMZSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CC(/CCC=C(CF)CF)=C\CCC(/C)=C/CO[P@@](O)(=O)O[P](O)(O)=O
ACDLabs 10.04FC/C(=C\CCC(=C\CC/C(=C/COP(=O)(OP(=O)(O)O)O)C)\C)CF
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCOP(=O)(O)OP(=O)(O)O)C)CCC=C(CF)CF
OpenEye OEToolkits 1.5.0C/C(=C\CC/C(=C/CO[P@](=O)(O)OP(=O)(O)O)/C)/CCC=C(CF)CF
CACTVS 3.341CC(CCC=C(CF)CF)=CCCC(C)=CCO[P](O)(=O)O[P](O)(O)=O
FormulaC15 H26 F2 O7 P2
Name(2E,6E)-12-fluoro-11-(fluoromethyl)-3,7-dimethyldodeca-2,6,10-trien-1-yl trihydrogen diphosphate
ChEMBL
DrugBank
ZINCZINC000064446573
PDB chain6wkd Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6wkd Mechanism Underlying Anti-Markovnikov Addition in the Reaction of Pentalenene Synthase.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		F76 F77 Y146 R173 I177 N219 W308 R314 Y315
Binding residue
(residue number reindexed from 1)		F68 F69 Y138 R158 I162 N204 W273 R279 Y280
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) F76 F77 I177 R314
Catalytic site (residue number reindexed from 1) F68 F69 I162 R279
Enzyme Commision number 4.2.3.7: pentalenene synthase.
Gene Ontology
Molecular Function
GO:0016829 lyase activity
GO:0046872 metal ion binding
GO:0050467 pentalenene synthase activity
Biological Process
GO:0017000 antibiotic biosynthetic process

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6wkd, PDBe:6wkd, PDBj:6wkd
PDBsum6wkd
PubMed32786410
UniProtQ55012|PENA_STREX Pentalenene synthase (Gene Name=penA)

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