Structure of PDB 3elc Chain A Binding Site BS02

Receptor Information
>3elc Chain A (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 IDF01
InChIInChI=1S/C9H12FN3O5/c10-3-1-13(9(17)12-7(3)11)8-6(16)5(15)4(2-14)18-8/h1,4-6,8,14-16H,2H2,(H2,11,12,17)/t4-,5-,6-,8-/m1/s1
InChIKeySTRZQWQNZQMHQR-UAKXSSHOSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1F)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O
ACDLabs 10.04FC=1C(=NC(=O)N(C=1)C2OC(C(O)C2O)CO)N
OpenEye OEToolkits 1.5.0C1=C(C(=NC(=O)N1C2C(C(C(O2)CO)O)O)N)F
CACTVS 3.341NC1=NC(=O)N(C=C1F)[CH]2O[CH](CO)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=C(C(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O)N)F
FormulaC9 H12 F N3 O5
Name4-amino-1-[(2R,3R,4S,5R)-3,4-dihydroxy-5-(hydroxymethyl)oxolan-2-yl]-5-fluoro-pyrimidin-2-one;
4-amino-5-fluoro-1-((2R,3S,4R,5R)-tetrahydro-3,4-dihydroxy-5-(hydroxymethyl)furan-2-yl)pyrimidin-2(1H)-one
ChEMBLCHEMBL490033
DrugBank
ZINCZINC000004255900
PDB chain3elc Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3elc A structure-based approach to ligand discovery for 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase: a target for antimicrobial therapy
Resolution2.5 Å
Binding residue
(original residue number in PDB)		A100 K104 M105 L106 A131 T132 T133
Binding residue
(residue number reindexed from 1)		A101 K105 M106 L107 A132 T133 T134
Annotation score1
Binding affinityMOAD: Kd=2.02mM
PDBbind-CN: -logKd/Ki=2.69,Kd=2.02mM
BindingDB: Kd=2020000nM
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:3elc, PDBe:3elc, PDBj:3elc
PDBsum3elc
PubMed19320487
UniProtP62617|ISPF_ECOLI 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

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