Structure of PDB 3ern Chain D Binding Site BS03

Receptor Information
>3ern Chain D (length=157) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDALL
GAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVTII
AQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIACE
AVALLIK
Ligand information
Ligand IDGPP
InChIInChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+
InChIKeyGVVPGTZRZFNKDS-JXMROGBWSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=CCCC(=CCOP(=O)(O)OP(=O)(O)O)C)C
OpenEye OEToolkits 1.5.0CC(=CCC/C(=C/CO[P@@](=O)(O)OP(=O)(O)O)/C)C
CACTVS 3.341CC(C)=CCCC(/C)=C/CO[P@](O)(=O)O[P](O)(O)=O
CACTVS 3.341CC(C)=CCCC(C)=CCO[P](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(OP(=O)(OC/C=C(/CC\C=C(/C)C)C)O)(O)O
FormulaC10 H20 O7 P2
NameGERANYL DIPHOSPHATE
ChEMBLCHEMBL41342
DrugBankDB02552
ZINCZINC000008215849
PDB chain3ern Chain F Residue 902 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ern A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy
Resolution2.1 Å
Binding residue
(original residue number in PDB)		G138 F139 R142
Binding residue
(residue number reindexed from 1)		G139 F140 R143
Annotation score1
Enzymatic activity
Enzyme Commision number 4.6.1.12: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0008270 zinc ion binding
GO:0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
GO:0016829 lyase activity
GO:0030145 manganese ion binding
GO:0042802 identical protein binding
GO:0046872 metal ion binding
Biological Process
GO:0006744 ubiquinone biosynthetic process
GO:0008299 isoprenoid biosynthetic process
GO:0016114 terpenoid biosynthetic process
GO:0019288 isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3ern, PDBe:3ern, PDBj:3ern
PDBsum3ern
PubMed19320487
UniProtP62617|ISPF_ECOLI 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

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