Structure of PDB 3dyf Chain B Binding Site BS03

Receptor Information
>3dyf Chain B (length=358) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNR
GLTVIDVAESLLSLDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNS
VTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLC
RFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIV
KYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMD
CFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEK
VATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLW
GKTYKRQK
Ligand information
Ligand IDNI9
InChIInChI=1S/C7H10FNO7P2/c8-6-2-1-3-9(4-6)5-7(10,17(11,12)13)18(14,15)16/h1-4,10H,5H2,(H3-,11,12,13,14,15,16)/p+1
InChIKeyLSEAIOLITUIQJU-UHFFFAOYSA-O
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)CC(O)(P(=O)(O)O)P(=O)(O)O)F
CACTVS 3.341OC(C[n+]1cccc(F)c1)([P](O)(O)=O)[P](O)(O)=O
ACDLabs 10.04Fc1ccc[n+](c1)CC(O)(P(=O)(O)O)P(=O)(O)O
FormulaC7 H11 F N O7 P2
Name3-FLUORO-1-(2-HYDROXY-2,2-DIPHOSPHONOETHYL)PYRIDINIUM
ChEMBL
DrugBank
ZINCZINC000013643058
PDB chain3dyf Chain B Residue 4001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dyf Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation.
Resolution2.65 Å
Binding residue
(original residue number in PDB)		D103 D107 R112 Q172 K212 D255 K269
Binding residue
(residue number reindexed from 1)		D94 D98 R103 Q163 K203 D246 K260
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K47 H98 D103 D107 R112 D175 K212 F251 D255 D256
Catalytic site (residue number reindexed from 1) K47 H89 D94 D98 R103 D166 K203 F242 D246 D247
Enzyme Commision number 2.5.1.10: (2E,6E)-farnesyl diphosphate synthase.
Gene Ontology
Molecular Function
GO:0004161 dimethylallyltranstransferase activity
GO:0004337 geranyltranstransferase activity
GO:0004659 prenyltransferase activity
GO:0016740 transferase activity
GO:0016765 transferase activity, transferring alkyl or aryl (other than methyl) groups
GO:0046872 metal ion binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0045337 farnesyl diphosphate biosynthetic process
Cellular Component
GO:0005737 cytoplasm

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3dyf, PDBe:3dyf, PDBj:3dyf
PDBsum3dyf
PubMed19309137
UniProtQ86C09

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