Structure of PDB 4dpt Chain B Binding Site BS01

Receptor Information
>4dpt 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]
VKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVTFDP
DFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYVPTA
AGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFA
EWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNVSSRSGMSLTRDTSRF
YQYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFT
YLVQESYDAMAIVEQCRKANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFL
KVFDESKIIASDIISSGVEIIK
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 chain4dpt Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4dpt Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase.
Resolution2.191 Å
Binding residue
(original residue number in PDB)		A14 Y18 K21 S139 G140 S141 R144 R193 M196 D283
Binding residue
(residue number reindexed from 1)		A13 Y17 K20 S138 G139 S140 R143 R188 M191 D278
Annotation score3
Binding affinityPDBbind-CN: -logKd/Ki=7.30,Ki=50nM
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:4dpt, PDBe:4dpt, PDBj:4dpt
PDBsum4dpt
PubMed22734632
UniProtQ9FD73

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