Structure of PDB 3k2x Chain C Binding Site BS01

Receptor Information
>3k2x Chain C (length=147) Species: 320372 (Burkholderia pseudomallei 1710b) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MDFRIGQGYDVHQLVPGRPLIIGGVTIPYERGLLGDADVLLHAITDALFG
AAALGDIGRHFDSRALLRECASRVAQAGFAIRNVDSTIIAQAPKLAPHID
AMRANIAADLDLPLDRVNVKAKTNEKLGYLGRGEGIEAQAAALVVRE
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 A Residue 164 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		D58 G60
Binding residue
(residue number reindexed from 1)		D56 G58
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)

[Back to BioLiP]