Structure of PDB 4du8 Chain A Binding Site BS01

Receptor Information
>4du8 Chain A (length=330) Species: 1282 (Staphylococcus epidermidis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
TGSMVKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKV
TFDPDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENY
VPTAAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIF
GGFAEWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNQSKKVSSRSGMS
LTRDTSRFYQYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATN
LGAQPPFTYLVQESYDAMAIVEQCRKANLPCYFTMAAGPNVKVLVEKKNK
QAVMEQFLKVFDESKIIASDIISSGVEIIK
Ligand information
Ligand ID2P0
InChIInChI=1S/C7H13NO10P2/c9-6(8-3-1-2-5(8)7(10)11)4-17-20(15,16)18-19(12,13)14/h5H,1-4H2,(H,10,11)(H,15,16)(H2,12,13,14)/t5-/m0/s1
InChIKeyJFTJDUMMWOSHFL-YFKPBYRVSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC(=O)[C@@H]1CCCN1C(=O)CO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.7.0C1CC(N(C1)C(=O)COP(=O)(O)OP(=O)(O)O)C(=O)O
ACDLabs 12.01O=C(N1C(C(=O)O)CCC1)COP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.0C1C[C@H](N(C1)C(=O)CO[P@](=O)(O)OP(=O)(O)O)C(=O)O
CACTVS 3.370OC(=O)[CH]1CCCN1C(=O)CO[P](O)(=O)O[P](O)(O)=O
FormulaC7 H13 N O10 P2
Name1-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}acetyl)-L-proline;
diphosphoglycolylproline
ChEMBLCHEMBL1160294
DrugBank
ZINCZINC000095539351
PDB chain4du8 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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PDB4du8 Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		A14 K17 Y18 K21 S139 G140 S141 R144 S192 R193 A283
Binding residue
(residue number reindexed from 1)		A17 K20 Y21 K24 S142 G143 S144 R147 S195 R196 A286
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.37,Ki=4.3uM
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:4du8, PDBe:4du8, PDBj:4du8
PDBsum4du8
PubMed22734632
UniProtQ9FD73

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