Structure of PDB 1yv5 Chain A Binding Site BS04

Receptor Information

>1yv5 Chain A (length=336) Species: 9606 (Homo sapiens)

EKQDFVQHFSQIVRVLTEDEHPEIGDAIARLKEVLEYNAIGGKYNRGLTV
VVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLTRRG
QICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFLQSS
YQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIAAAM
YMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTDIQD
NKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLPAVF
LQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK

Ligand information

• Ligand ID: PO4
• InChI: InChI=1S/H3O4P/c1-5(2,3)4/h(H3,1,2,3,4)/p-3
• InChIKey: NBIIXXVUZAFLBC-UHFFFAOYSA-K
• SMILES:
  CACTVS 3.341: [O-][P]([O-])([O-])=O
  ACDLabs 10.04: [O-]P([O-])([O-])=O
  OpenEye OEToolkits 1.5.0: [O-]P(=O)([O-])[O-]
• Formula: O4 P
• Name: PHOSPHATE ION
• DrugBank: DB14523
• PDB chain: 1yv5 Chain A Residue 1002

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1yv5 The molecular mechanism of nitrogen-containing bisphosphonates as antiosteoporosis drugs.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): Q110 F253
• Binding residue (residue number reindexed from 1): Q82 F225
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): K71 F112 D117 D121 R126 D188 K214 F253 D257 D258
• Catalytic site (residue number reindexed from 1): K43 F84 D89 D93 R98 D160 K186 F225 D229 D230
• Enzyme Commision number: 2.5.1.1: dimethylallyltranstransferase.
  2.5.1.10: (2E,6E)-farnesyl diphosphate synthase.

Gene Ontology

Molecular Function

• GO:0004659 prenyltransferase activity
• GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups

Biological Process

• GO:0008299 isoprenoid biosynthetic process

External links

• PDB: RCSB:1yv5, PDBe:1yv5, PDBj:1yv5
• PDBsum: 1yv5
• PubMed: 16684881
• UniProt: P14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)