Structure of PDB 2pmp Chain A Binding Site BS02

Receptor Information

>2pmp Chain A (length=160) Species: 3702 (Arabidopsis thaliana)

TLPFRIGHGFDLHRLEPGYPLIIGGIVIPHDRGCEAHSDGDVLLHCVVDA
ILGALGLPDIGQIFPDSDPKWKGAASSVFIKEAVRLMDEAGYEIGNLDAT
LILQRPKISPHKETIRSNLSKLLGADPSVVNLKAKTHEKVDSLGENRSIA
AHTVILLMKK

Ligand information

• Ligand ID: C5P
• InChI: InChI=1S/C9H14N3O8P/c10-5-1-2-12(9(15)11-5)8-7(14)6(13)4(20-8)3-19-21(16,17)18/h1-2,4,6-8,13-14H,3H2,(H2,10,11,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
• InChIKey: IERHLVCPSMICTF-XVFCMESISA-N
• SMILES:
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[CH]2O[CH](CO[P](O)(O)=O)[CH](O)[CH]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)C2C(C(C(O2)COP(=O)(O)O)O)O
  CACTVS 3.341: NC1=NC(=O)N(C=C1)[C@@H]2O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]2O
  OpenEye OEToolkits 1.5.0: C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
  ACDLabs 10.04: O=C1N=C(N)C=CN1C2OC(C(O)C2O)COP(=O)(O)O
• Formula: C9 H14 N3 O8 P
• Name: CYTIDINE-5'-MONOPHOSPHATE
• ChEMBL: CHEMBL307679
• DrugBank: DB03403
• ZINC: ZINC000003861744
• PDB chain: 2pmp Chain A Residue 700

Receptor-Ligand Complex Structure

Structure summary

• PDB: 2pmp Biosynthesis of isoprenoids in plants: Structure of the 2C-methyl-D-erithrytol 2,4-cyclodiphosphate synthase from Arabidopsis thaliana. Comparison with the bacterial enzymes.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): D59 G61
• Binding residue (residue number reindexed from 1): D59 G61
• Annotation score: 3

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

Biological Process

• GO:0016114 terpenoid biosynthetic process

External links

• PDB: RCSB:2pmp, PDBe:2pmp, PDBj:2pmp
• PDBsum: 2pmp
• PubMed: 17660251
• UniProt: Q9CAK8|ISPF_ARATH 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, chloroplastic (Gene Name=ISPF)