Structure of PDB 3p10 Chain A Binding Site BS02

Receptor Information
>3p10 Chain A (length=159) Species: 320372 (Burkholderia pseudomallei 1710b) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGHSDADVLLHAITDAL
FGAAALGDIGRHFSDTDPRFKGADSRALLRECASRVAQAGFAIRNVDSTI
IAQAPKLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEA
QAAALVVRE
Ligand information
Ligand IDCTN
InChIInChI=1S/C9H13N3O5/c10-5-1-2-12(9(16)11-5)8-7(15)6(14)4(3-13)17-8/h1-2,4,6-8,13-15H,3H2,(H2,10,11,16)/t4-,6-,7-,8-/m1/s1
InChIKeyUHDGCWIWMRVCDJ-XVFCMESISA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O
ACDLabs 10.04O=C1N=C(N)C=CN1C2OC(C(O)C2O)CO
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)CO)O)O
FormulaC9 H13 N3 O5
Name4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE;
CYTIDINE
ChEMBLCHEMBL95606
DrugBankDB02097
ZINCZINC000002583632
PDB chain3p10 Chain A Residue 165 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3p10 Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		A102 K106 L107 A108 A133 K134
Binding residue
(residue number reindexed from 1)		A102 K106 L107 A108 A133 K134
Annotation score2
Enzymatic activity
Enzyme Commision number 4.6.1.12: 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase.
Gene Ontology
Molecular Function
GO:0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity
GO:0016829 lyase activity
GO:0046872 metal ion binding
Biological 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:3p10, PDBe:3p10, PDBj:3p10
PDBsum3p10
PubMed21359640
UniProtQ3JRA0|ISPF_BURP1 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

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