Structure of PDB 4du7 Chain B Binding Site BS01

Receptor Information
>4du7 Chain B (length=322) Species: 1282 (Staphylococcus epidermidis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVTFD
PDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYVPT
AAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGF
AEWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNVSSRSGMSLTRDTSR
FYQYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPF
TYLVQESYDAMAIVEQCRKANLPCYFTMDAGPNVKVLVEKKNKQAVMEQF
LKVFDESKIIASDIISSGVEII
Ligand information
Ligand IDDP6
InChIInChI=1S/C6H14O10P2/c1-6(9,4-5(7)8)2-3-15-18(13,14)16-17(10,11)12/h9H,2-4H2,1H3,(H,7,8)(H,13,14)(H2,10,11,12)/t6-/m1/s1
InChIKeySIGQQUBJQXSAMW-ZCFIWIBFSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C[C@@](CCO[P@@](=O)(O)OP(=O)(O)O)(CC(=O)O)O
ACDLabs 10.04O=P(OP(=O)(OCCC(O)(C)CC(=O)O)O)(O)O
OpenEye OEToolkits 1.5.0CC(CCOP(=O)(O)OP(=O)(O)O)(CC(=O)O)O
CACTVS 3.341C[C@@](O)(CCO[P@](O)(=O)O[P](O)(O)=O)CC(O)=O
CACTVS 3.341C[C](O)(CCO[P](O)(=O)O[P](O)(O)=O)CC(O)=O
FormulaC6 H14 O10 P2
Name(3R)-3-HYDROXY-5-{[(R)-HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}-3-METHYLPENTANOIC ACID
ChEMBLCHEMBL235881
DrugBank
ZINCZINC000008216889
PDB chain4du7 Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4du7 Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase.
Resolution2.201 Å
Binding residue
(original residue number in PDB)		A14 Y18 W19 K21 S139 G140 S141 R144 S192 R193 M196 D283
Binding residue
(residue number reindexed from 1)		A14 Y18 W19 K21 S139 G140 S141 R144 S188 R189 M192 D279
Annotation score5
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4du7, PDBe:4du7, PDBj:4du7
PDBsum4du7
PubMed22734632
UniProtQ9FD73

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