Structure of PDB 1iv2 Chain D Binding Site BS03

Receptor Information
>1iv2 Chain D (length=150) Species: 274 (Thermus thermophilus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RIGYGEDSHRLEEGRPLYLCGLLIPSPVGALAHSDGDAAMHALTDALLSA
YGLGDIGLLFPDTDPRWRGERSEVFLREAMRLVEARGAKLLQASLVLTLD
RPKLGPHRKALVDSLSRLMRLPQDRIGLTFKTSEGLAPSHVQARAVVLLD
Ligand information
Ligand IDCDP
InChIInChI=1S/C9H15N3O11P2/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyZWIADYZPOWUWEW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]2O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)C(O)C2O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.341NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]2O
FormulaC9 H15 N3 O11 P2
NameCYTIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL425252
DrugBankDB04555
ZINCZINC000008215624
PDB chain1iv2 Chain E Residue 1605 [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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PDB1iv2 Structure and catalytic mechanism of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MECDP) synthase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		L1100 K1104 L1105 G1106 F1131 K1132 T1133 E1135
Binding residue
(residue number reindexed from 1)		L99 K103 L104 G105 F130 K131 T132 E134
Annotation score3
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:1iv2, PDBe:1iv2, PDBj:1iv2
PDBsum1iv2
PubMed12499535
UniProtQ8RQP5|ISPF_THET8 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (Gene Name=ispF)

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