Structure of PDB 3dyh Chain B Binding Site BS03

Receptor Information
>3dyh Chain B (length=359) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNR
GLTVIDVAESLLSLDDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDN
SVTRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLL
CRFNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRI
VKYKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVM
DCFTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSE
KVATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETL
WGKTYKRQK
Ligand information
Ligand ID721
InChIInChI=1S/C11H19NO7P2/c1-2-3-7-19-10-5-4-6-12(8-10)9-11(20(13,14)15)21(16,17)18/h4-6,8,11H,2-3,7,9H2,1H3,(H3-,13,14,15,16,17,18)/p+1
InChIKeyNGZGWCCNSBOMDA-UHFFFAOYSA-O
SMILES
SoftwareSMILES
ACDLabs 10.04O=P(O)(O)C(P(=O)(O)O)C[n+]1cccc(OCCCC)c1
OpenEye OEToolkits 1.5.0CCCCOc1ccc[n+](c1)CC(P(=O)(O)O)P(=O)(O)O
CACTVS 3.341CCCCOc1ccc[n+](CC([P](O)(O)=O)[P](O)(O)=O)c1
FormulaC11 H20 N O7 P2
Name3-butoxy-1-(2,2-diphosphonoethyl)pyridinium
ChEMBL
DrugBank
ZINCZINC000058631251
PDB chain3dyh 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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PDB3dyh Lipophilic bisphosphonates as dual farnesyl/geranylgeranyl diphosphate synthase inhibitors: an X-ray and NMR investigation.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		Y99 D103 R112 T168 A169 Q172 K212 D255 K269
Binding residue
(residue number reindexed from 1)		Y91 D95 R104 T160 A161 Q164 K204 D247 K261
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 H90 D95 D99 R104 D167 K204 F243 D247 D248
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:3dyh, PDBe:3dyh, PDBj:3dyh
PDBsum3dyh
PubMed19309137
UniProtQ86C09

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