Structure of PDB 5dgm Chain F Binding Site BS01

Receptor Information
>5dgm 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 ID59Z
InChIInChI=1S/C16H15N2O6P/c19-14(20)8-18-13(16(21)17-9-25(22,23)24)7-11-6-5-10-3-1-2-4-12(10)15(11)18/h1-7H,8-9H2,(H,17,21)(H,19,20)(H2,22,23,24)
InChIKeyJUZJWGPHICAWME-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C(NC(c2cc3ccc1c(cccc1)c3n2CC(O)=O)=O)P(O)(=O)O
CACTVS 3.385OC(=O)Cn1c(cc2ccc3ccccc3c12)C(=O)NC[P](O)(O)=O
OpenEye OEToolkits 1.9.2c1ccc2c(c1)ccc3c2n(c(c3)C(=O)NCP(=O)(O)O)CC(=O)O
FormulaC16 H15 N2 O6 P
Name{2-[(phosphonomethyl)carbamoyl]-1H-benzo[g]indol-1-yl}acetic acid
ChEMBL
DrugBank
ZINCZINC000584904794
PDB chain5dgm Chain F Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5dgm A General Strategy for Targeting Drugs to Bone.
Resolution2.86 Å
Binding residue
(original residue number in PDB)		Y10 K57 N59 R60 F206 F239 L344 I348
Binding residue
(residue number reindexed from 1)		Y3 K50 N52 R53 F199 F232 L337 I341
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.40,IC50=0.4uM
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:5dgm, PDBe:5dgm, PDBj:5dgm
PDBsum5dgm
PubMed26457482
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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