Structure of PDB 4h5d Chain F Binding Site BS01

Receptor Information
>4h5d Chain F (length=346) 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
LDLPAVFLQYEEDSYSHIMALIEQYAAPLPPAVFLGLARKIYKRRK
Ligand information
Ligand IDYS4
InChIInChI=1S/C15H20N2O7P2/c1-10(2)24-13-5-3-11(4-6-13)12-7-8-16-14(9-12)17-15(25(18,19)20)26(21,22)23/h3-10,15H,1-2H3,(H,16,17)(H2,18,19,20)(H2,21,22,23)
InChIKeyDTXBFSJBRGLOHO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)Oc1ccc(cc1)c2ccnc(NC([P](O)(O)=O)[P](O)(O)=O)c2
OpenEye OEToolkits 1.7.6CC(C)Oc1ccc(cc1)c2ccnc(c2)NC(P(=O)(O)O)P(=O)(O)O
ACDLabs 12.01O=P(O)(O)C(Nc1nccc(c1)c2ccc(OC(C)C)cc2)P(=O)(O)O
FormulaC15 H20 N2 O7 P2
Name[({4-[4-(propan-2-yloxy)phenyl]pyridin-2-yl}amino)methanediyl]bis(phosphonic acid)
ChEMBLCHEMBL2048241
DrugBank
ZINCZINC000084668835
PDB chain4h5d Chain F Residue 401 [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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PDB4h5d Ternary complex structures of human farnesyl pyrophosphate synthase bound with a novel inhibitor and secondary ligands provide insights into the molecular details of the enzyme's active site closure.
Resolution2.02 Å
Binding residue
(original residue number in PDB)		F99 D103 R112 T167 E168 Q171 K200 D243 K257
Binding residue
(residue number reindexed from 1)		F92 D96 R105 T160 E161 Q164 K193 D236 K250
Annotation score1
Binding affinityMOAD: Kd=0.58uM
PDBbind-CN: -logKd/Ki=7.55,IC50=28nM
BindingDB: IC50=28nM
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:4h5d, PDBe:4h5d, PDBj:4h5d
PDBsum4h5d
PubMed23234314
UniProtP14324|FPPS_HUMAN Farnesyl pyrophosphate synthase (Gene Name=FDPS)

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