Structure of PDB 3q1o Chain D Binding Site BS03

Receptor Information

>3q1o Chain D (length=299) Species: 210 (Helicobacter pylori)

SSPNLSFYYNECERFESFLKNHHLHLESFHPYLEKAFFEMVLNGGKRFRP
KLFLAVLCALVGQKDYSNQQTEYFKIALSIECLHTYSLIHDDLPCMDNAA
LRRNHPTLHAKYDETTAVLIGDALNTYSFELLSNALLESHIIVELIKILS
ANGGIKGMILGQALDCYFENTPLNLEQLTFLHEHKTAKLISASLIMGLVA
SGIKDEELFKWLQAFGLKMGLCFQVLDDIIDVTQDEEESGKTTHLDSAKN
SFVNLLGLERANNYAQTLKTEVLNDLDALKPAYPLLQENLNALLNTLFK

Ligand information

• Ligand ID: DMA
• InChI: InChI=1S/C5H12O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h3H,4H2,1-2H3,(H,9,10)(H2,6,7,8)
• InChIKey: CBIDRCWHNCKSTO-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: CC(=CCOP(=O)(O)OP(=O)(O)O)C
  ACDLabs 10.04: O=P(OP(=O)(OC/C=C(/C)C)O)(O)O
  OpenEye OEToolkits 1.5.0: CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C
  CACTVS 3.341: CC(C)=CCO[P@](O)(=O)O[P](O)(O)=O
  CACTVS 3.341: CC(C)=CCO[P](O)(=O)O[P](O)(O)=O
• Formula: C5 H12 O7 P2
• Name: DIMETHYLALLYL DIPHOSPHATE
• ChEMBL: CHEMBL343480
• DrugBank: DB01785
• ZINC: ZINC000008215740
• PDB chain: 3q1o Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3q1o Prediction of function for the polyprenyl transferase subgroup in the isoprenoid synthase superfamily.
• Resolution: 2.4 Å
• Binding residue (original residue number in PDB): S88 D92 R103 M159 K186 K242
• Binding residue (residue number reindexed from 1): S87 D91 R102 M158 K185 K241
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0004659 prenyltransferase activity
• GO:0016740 transferase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0008299 isoprenoid biosynthetic process

External links

• PDB: RCSB:3q1o, PDBe:3q1o, PDBj:3q1o
• PDBsum: 3q1o
• PubMed: 23493556
• UniProt: O25583