Structure of PDB 3k2x Chain B Binding Site BS02

Receptor Information
>3k2x Chain B (length=153) Species: 320372 (Burkholderia pseudomallei 1710b) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGDADVLLHAITDALFG
AAALGDIGRHFSDTDPRADSRALLRECASRVAQAGFAIRNVDSTIIAQAP
KLAPHIDAMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAAL
VVR
Ligand information
Ligand IDI5A
InChIInChI=1S/C9H12IN3O4/c10-3-4-6(14)7(15)8(17-4)13-2-1-5(11)12-9(13)16/h1-2,4,6-8,14-15H,3H2,(H2,11,12,16)/t4-,6-,7-,8-/m1/s1
InChIKeyZFSSJWRSRMQVTI-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CI)O)O
ACDLabs 11.02O=C1N=C(N)C=CN1C2OC(C(O)C2O)CI
OpenEye OEToolkits 1.7.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)CI)O)O
CACTVS 3.352NC1=NC(=O)N(C=C1)[CH]2O[CH](CI)[CH](O)[CH]2O
CACTVS 3.352NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CI)[C@@H](O)[C@H]2O
FormulaC9 H12 I N3 O4
Name5'-deoxy-5'-iodocytidine
ChEMBL
DrugBank
ZINCZINC000058633354
PDB chain3k2x Chain B Residue 164 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3k2x Leveraging structure determination with fragment screening for infectious disease drug targets: MECP synthase from Burkholderia pseudomallei.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		L107 A108 A133 K134 T135
Binding residue
(residue number reindexed from 1)		L102 A103 A128 K129 T130
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:3k2x, PDBe:3k2x, PDBj:3k2x
PDBsum3k2x
PubMed21359640
UniProtQ3JRA0|ISPF_BURP1 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

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