Structure of PDB 5jv0 Chain F Binding Site BS03

Receptor Information
>5jv0 Chain F (length=341) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVYAQEKQDFVQHFSQIVRVLTEDEMGHPEIGDAIARLKEVLEYNAIGGK
YNRGLTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMD
SSLTRRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLI
ELFLQSSYQTEIGQTLDLLTAPNVDLVRFTEKRYKSIVKYKTAFYSFYLP
IAAAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIG
TDIQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELD
LPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYK
Ligand information
Ligand IDYL5
InChIInChI=1S/C21H19FN3O3PS/c1-13-5-7-15(8-6-13)18-11-17-20(23-12-24-21(17)30-18)25-19(29(26,27)28)10-14-3-2-4-16(22)9-14/h2-9,11-12,19H,10H2,1H3,(H,23,24,25)(H2,26,27,28)/t19-/m1/s1
InChIKeyASWGUDOBPNZODI-LJQANCHMSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ccc(cc1)c2sc3ncnc(N[C@@H](Cc4cccc(F)c4)[P](O)(O)=O)c3c2
ACDLabs 12.01c1c(cccc1F)CC(P(O)(=O)O)Nc2ncnc3c2cc(s3)c4ccc(cc4)C
CACTVS 3.385Cc1ccc(cc1)c2sc3ncnc(N[CH](Cc4cccc(F)c4)[P](O)(O)=O)c3c2
OpenEye OEToolkits 2.0.4Cc1ccc(cc1)c2cc3c(ncnc3s2)N[C@@H](Cc4cccc(c4)F)P(=O)(O)O
OpenEye OEToolkits 2.0.4Cc1ccc(cc1)c2cc3c(ncnc3s2)NC(Cc4cccc(c4)F)P(=O)(O)O
FormulaC21 H19 F N3 O3 P S
Name[(1R)-2-(3-fluorophenyl)-1-{[6-(4-methylphenyl)thieno[2,3-d]pyrimidin-4-yl]amino}ethyl]phosphonic acid
ChEMBLCHEMBL4550499
DrugBank
ZINC
PDB chain5jv0 Chain F Residue 405 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB5jv0 Pharmacophore Mapping of Thienopyrimidine-Based Monophosphonate (ThP-MP) Inhibitors of the Human Farnesyl Pyrophosphate Synthase.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Y322 Y349 K350
Binding residue
(residue number reindexed from 1)		Y313 Y340 K341
Annotation score1
Binding affinityMOAD: ic50=1.1uM
PDBbind-CN: -logKd/Ki=5.96,IC50=1.1uM
BindingDB: IC50=1100nM
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:5jv0, PDBe:5jv0, PDBj:5jv0
PDBsum5jv0
PubMed28208018
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

[Back to BioLiP]