Structure of PDB 3qt6 Chain B Binding Site BS01

Receptor Information
>3qt6 Chain B (length=321) Species: 1282 (Staphylococcus epidermidis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MVKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVTFD
PDFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYVPT
AAGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGF
AEWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNSRSGMSLTRDTSRFY
QYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFTY
LVQESYDAMAIVEQCRKANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFLK
VFDESKIIASDIISSGVEIIK
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 chain3qt6 Chain B Residue 328 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qt6 Crystal structures of Staphylococcus epidermidis mevalonate diphosphate decarboxylase bound to inhibitory analogs reveal new insight into substrate binding and catalysis.
Resolution2.047 Å
Binding residue
(original residue number in PDB)		K17 Y18 K21 S139 G140 S141 R144 S192 R193 D283
Binding residue
(residue number reindexed from 1)		K17 Y18 K21 S139 G140 S141 R144 S186 R187 D277
Annotation score1
Binding affinityMOAD: 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:3qt6, PDBe:3qt6, PDBj:3qt6
PDBsum3qt6
PubMed21561869
UniProtQ9FD73

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