Structure of PDB 3esj Chain A Binding Site BS02

Receptor Information
>3esj Chain A (length=162) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLEMRIGHGFDVHAFGGEGPIIIGGVRIPYEKGLLAHSDGDVALHALTDA
LLGAAALGDIGKLFPDTDPAFKGADSRELLREAWRRIQAKGYTLGNVDVT
IIAQAPKMLPHIPQMRVFIAEDLGCHMDDVNVKATTTEKLGFTGRGEGIA
CEAVALLIKATK
Ligand information
Ligand IDCC7
InChIInChI=1S/C9H12N3O7P/c10-5-1-2-12(9(14)11-5)8-6(13)7-4(18-8)3-17-20(15,16)19-7/h1-2,4,6-8,13H,3H2,(H,15,16)(H2,10,11,14)/t4-,6-,7-,8-/m1/s1
InChIKeyWCPTXJJVVDAEMW-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH]3CO[P](O)(=O)O[CH]3[CH]2O
OpenEye OEToolkits 1.5.0C1[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=NC3=O)N)O)O[P@](=O)(O1)O
OpenEye OEToolkits 1.5.0C1C2C(C(C(O2)N3C=CC(=NC3=O)N)O)OP(=O)(O1)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@@H]3CO[P@@](O)(=O)O[C@H]3[C@H]2O
ACDLabs 10.04O=C1N=C(N)C=CN1C3OC2COP(=O)(OC2C3O)O
FormulaC9 H12 N3 O7 P
Name4-amino-1-[(2S,4aR,6R,7R,7aS)-2,7-dihydroxy-2-oxidotetrahydro-4H-furo[3,2-d][1,3,2]dioxaphosphinin-6-yl]pyrimidin-2(1H)-one
ChEMBLCHEMBL72442
DrugBank
ZINCZINC000004095499
PDB chain3esj Chain A Residue 901 [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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PDB3esj A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy
Resolution2.7 Å
Binding residue
(original residue number in PDB)		A100 K104 M105 L106 A131 T133
Binding residue
(residue number reindexed from 1)		A103 K107 M108 L109 A134 T136
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.03,Kd=0.925mM
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:3esj, PDBe:3esj, PDBj:3esj
PDBsum3esj
PubMed19320487
UniProtP62617|ISPF_ECOLI 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

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