Structure of PDB 5nx5 Chain A Binding Site BS01

Receptor Information
>5nx5 Chain A (length=287) Species: 1901 (Streptomyces clavuligerus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RVSPDLARARARHLDWVHAMDLVRGEEARRRYEFSCVADIGAYGYPHATG
ADLDLCVDVLGWTFLFDDQFDRERDALAVCAELTDLLWKGTAATAASPPI
VVAFSDCWERMRAGMSDAWRRRTVHEWVDYLAGWPTKLADRAHGAVLDPA
AHLRARHRTICCRPLFALAERVGGYEVPRRAWHSSRLDGMRFTTSDAVIG
MNELHSFEKDRAQHANLVLSLVHHGGLTGPEAVTRVCDLVQGSIESFLRL
RSGLPELGRALGVEGAVLDRYADALSAFCRGYHDWGR
Ligand information
Ligand ID0FV
InChIInChI=1S/C10H19FO7P2/c1-8(2)5-4-6-9(3)10(11)7-17-20(15,16)18-19(12,13)14/h5H,4,6-7H2,1-3H3,(H,15,16)(H2,12,13,14)/b10-9-
InChIKeyBYJNSLXDWGDGAC-KTKRTIGZSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)=CCCC(C)=C(F)CO[P](O)(=O)O[P](O)(O)=O
ACDLabs 12.01O=P(O)(O)OP(=O)(OCC(\F)=C(/C)CC\C=C(/C)C)O
OpenEye OEToolkits 1.7.6CC(=CCC/C(=C(/COP(=O)(O)OP(=O)(O)O)\F)/C)C
CACTVS 3.370CC(C)=CCCC(/C)=C(F)/CO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.7.6CC(=CCCC(=C(COP(=O)(O)OP(=O)(O)O)F)C)C
FormulaC10 H19 F O7 P2
Name(2Z)-2-fluoro-3,7-dimethylocta-2,6-dien-1-yl trihydrogen diphosphate;
2-fluorogeranyl diphosphate
ChEMBL
DrugBank
ZINC
PDB chain5nx5 Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5nx5 Structural Basis of Catalysis in the Bacterial Monoterpene Synthases Linalool Synthase and 1,8-Cineole Synthase.
Resolution1.82 Å
Binding residue
(original residue number in PDB)
F76 D79 N218 K225
Binding residue
(residue number reindexed from 1)
F64 D67 N202 K209
Annotation score3
Enzymatic activity
Catalytic site (original residue number in PDB) T75 F76 D79 D83 R157 R172 N218 S222 K225 D226 Q229 W302 G303
Catalytic site (residue number reindexed from 1) T63 F64 D67 D71 R141 R156 N202 S206 K209 D210 Q213 W285 G286
Enzyme Commision number 4.2.3.26: R-linalool synthase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0016829 lyase activity
GO:0034008 R-linalool synthase activity
GO:0046872 metal ion binding
Biological Process
GO:0033383 geranyl diphosphate metabolic process
GO:0045338 farnesyl diphosphate metabolic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:5nx5, PDBe:5nx5, PDBj:5nx5
PDBsum5nx5
PubMed28966840
UniProtD5SL78|LNSA_STRCL R-linalool synthase (Gene Name=SCLAV_p1185)

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