Structure of PDB 3n5h Chain F Binding Site BS02

Receptor Information
>3n5h Chain F (length=343) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGK
YNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMD
SSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLI
ELFLQSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFY
LPIAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGK
IGTDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEE
LDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK
Ligand information
Ligand IDGO0
InChIInChI=1S/C11H7Cl2NO4/c12-5-1-2-6(13)10-8(5)4(3-7(15)16)9(14-10)11(17)18/h1-2,14H,3H2,(H,15,16)(H,17,18)
InChIKeyGQXFZEWSJBOLCT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1cc(c2c(c1Cl)c(c([nH]2)C(=O)O)CC(=O)O)Cl
CACTVS 3.370OC(=O)Cc1c([nH]c2c(Cl)ccc(Cl)c12)C(O)=O
ACDLabs 12.01O=C(O)Cc2c1c(c(Cl)ccc1Cl)nc2C(=O)O
FormulaC11 H7 Cl2 N O4
Name3-(carboxymethyl)-4,7-dichloro-1H-indole-2-carboxylic acid
ChEMBL
DrugBank
ZINCZINC000058633010
PDB chain3n5h Chain F Residue 2 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3n5h Allosteric non-bisphosphonate FPPS inhibitors identified by fragment-based discovery.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		S109 L110 T111 T260 D264 K293
Binding residue
(residue number reindexed from 1)		S102 L103 T104 T253 D257 K286
Annotation score1
Binding affinityMOAD: ic50=2uM
PDBbind-CN: -logKd/Ki=5.70,IC50=2uM
BindingDB: IC50=2e+3nM
Enzymatic activity
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

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3n5h, PDBe:3n5h, PDBj:3n5h
PDBsum3n5h
PubMed20711197
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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