Structure of PDB 4dpw Chain E Binding Site BS02

Receptor Information
>4dpw Chain E (length=328) Species: 1282 (Staphylococcus epidermidis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSMVKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVT
FDPDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYV
PTAAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFG
GFAEWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNQSKKVSSRSGMSL
TRDTSRFYQYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNL
GAQPPFTYLVQESYDAMAIVEQCRKANLPCYFTMAAGPNVKVLVEKKNKQ
AVMEQFLKVFDESKIIASDIISSGVEII
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 chain4dpw Chain E Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4dpw Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase.
Resolution2.605 Å
Binding residue
(original residue number in PDB)		A14 K17 Y18 K21 S139 G140 S141 R193 M196 A283
Binding residue
(residue number reindexed from 1)		A16 K19 Y20 K23 S141 G142 S143 R195 M198 A285
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:4dpw, PDBe:4dpw, PDBj:4dpw
PDBsum4dpw
PubMed22734632
UniProtQ9FD73

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