Structure of PDB 5ygi Chain A Binding Site BS03

Receptor Information
>5ygi Chain A (length=338) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DVYAQEKQDFVQHFSQIVRVLTEHPEIGDAIARLKEVLEYNAIGGKYNRG
LTVVVAFRELVEPRKQDADSLQRAWTVGWCVELLQAFFLVADDIMDSSLT
RRGQICWYQKPGVGLDAINDANLLEACIYRLLKLYCREQPYYLNLIELFL
QSSYQTEIGQTLDLLTAPQGNVDLVRFTEKRYKSIVKYKTAFYSFYLPIA
AAMYMAGIDGEKEHANAKKILLEMGEFFQIQDDYLDLFGDPSVTGKIGTD
IQDNKCSWLVVQCLQRATPEQYQILKENYGQKEAEKVARVKALYEELDLP
AVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIY
Ligand information
Ligand IDT93
InChIInChI=1S/C12H22N2O7P2/c1-2-3-4-5-8-21-10-6-7-13-11(9-10)14-12(22(15,16)17)23(18,19)20/h6-7,9,12H,2-5,8H2,1H3,(H,13,14)(H2,15,16,17)(H2,18,19,20)
InChIKeyNXVHNJBPVOSZAP-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CCCCCCOc1ccnc(c1)NC(P(=O)(O)O)P(=O)(O)O
CACTVS 3.385CCCCCCOc1ccnc(NC([P](O)(O)=O)[P](O)(O)=O)c1
FormulaC12 H22 N2 O7 P2
Name[[(4-hexoxypyridin-2-yl)amino]-phosphono-methyl]phosphonic acid
ChEMBL
DrugBank
ZINC
PDB chain5ygi Chain A Residue 506 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB5ygi The Mevalonate Pathway Is a Druggable Target for Vaccine Adjuvant Discovery.
Resolution2.177 Å
Binding residue
(original residue number in PDB)		F98 F99 D103 M106 R112 Q171 K200 D243 K257
Binding residue
(residue number reindexed from 1)		F87 F88 D92 M95 R101 Q160 K189 D232 K246
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.05,IC50=90nM
Enzymatic activity
Catalytic site (original residue number in PDB) K57 F98 D103 D107 R112 D174 K200 F239 D243 D244
Catalytic site (residue number reindexed from 1) K46 F87 D92 D96 R101 D163 K189 F228 D232 D233
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:5ygi, PDBe:5ygi, PDBj:5ygi
PDBsum5ygi
PubMed30270039
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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