Structure of PDB 3qt7 Chain B Binding Site BS01

Receptor Information
>3qt7 Chain B (length=320) Species: 1282 (Staphylococcus epidermidis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVTFDP
DFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYVPTA
AGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFA
EWEKGHDDLTSYAHGINSNGWEKDLSMIFVVIVSSRSGMSLTRDTSRFYQ
YWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFTYL
VQESYDAMAIVEQCRKANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFLKV
FDESKIIASDIISSGVEIIK
Ligand information
Ligand IDFM0
InChIInChI=1S/C6H13FO10P2/c7-4-6(10,3-5(8)9)1-2-16-19(14,15)17-18(11,12)13/h10H,1-4H2,(H,8,9)(H,14,15)(H2,11,12,13)/t6-/m1/s1
InChIKeyYIGLDWRZXXHIGZ-ZCFIWIBFSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)OP(=O)(OCCC(O)(CC(=O)O)CF)O
OpenEye OEToolkits 1.7.0C(COP(=O)(O)OP(=O)(O)O)C(CC(=O)O)(CF)O
OpenEye OEToolkits 1.7.0C(CO[P@](=O)(O)OP(=O)(O)O)[C@@](CC(=O)O)(CF)O
CACTVS 3.370OC(=O)C[C](O)(CF)CCO[P](O)(=O)O[P](O)(O)=O
CACTVS 3.370OC(=O)C[C@@](O)(CF)CCO[P](O)(=O)O[P](O)(O)=O
FormulaC6 H13 F O10 P2
Name(3R)-3-(fluoromethyl)-3-hydroxy-5-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}pentanoic acid;
6-fluoromevalonate 5-diphosphate
ChEMBLCHEMBL1160328
DrugBank
ZINC
PDB chain3qt7 Chain B Residue 328 [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]
PDB3qt7 Crystal structures of Staphylococcus epidermidis mevalonate diphosphate decarboxylase bound to inhibitory analogs reveal new insight into substrate binding and catalysis.
Resolution2.199 Å
Binding residue
(original residue number in PDB)		A14 Y18 W19 K21 S139 G140 S141 R144 S192 R193 M196 D283 A284
Binding residue
(residue number reindexed from 1)		A13 Y17 W18 K20 S138 G139 S140 R143 S185 R186 M189 D276 A277
Annotation score3
Binding affinityMOAD: Ki=49uM
Enzymatic activity
Enzyme Commision number 4.1.1.33: diphosphomevalonate decarboxylase.
Gene Ontology
Molecular Function
GO:0004163 diphosphomevalonate decarboxylase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016829 lyase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0006629 lipid metabolic process
GO:0008299 isoprenoid biosynthetic process
GO:0016310 phosphorylation
GO:0019287 isopentenyl diphosphate biosynthetic process, mevalonate pathway
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3qt7, PDBe:3qt7, PDBj:3qt7
PDBsum3qt7
PubMed21561869
UniProtQ9FD73

[Back to BioLiP]