Structure of PDB 3dyf Chain A Binding Site BS04

Receptor Information
>3dyf Chain A (length=357) Species: 5691 (Trypanosoma brucei) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MPMQMFMQVYDEIQMFLLEELELKFDMDPNRVRYLRKMMDTTCLGGKYNR
GLTVIDVAESLLSDGARRKRVLHDACVCGWMIEFLQAHYLVEDDIMDNSV
TRRGKPCWYRHPDVTVQCAINDGLLLKSWTHMMAMHFFADRPFLQDLLCR
FNRVDYTTAVGQLYDVTSMFDSNKLDPDVSQPTTTDFAEFTLSNYKRIVK
YKTAYYTYLLPLVMGLIVSEALPTVDMGVTEELAMLMGEYFQVQDDVMDC
FTPPERLGKVGTDIQDAKCSWLAVTFLAKASSAQVAEFKANYGSGDSEKV
ATVRRLYEEADLQGDYVAYEAAVAEQVKELIEKLRLCSPGFAASVETLWG
KTYKRQK
Ligand information
Ligand IDIPR
InChIInChI=1S/C5H14O7P2/c1-5(2)3-4-11-14(9,10)12-13(6,7)8/h5H,3-4H2,1-2H3,(H,9,10)(H2,6,7,8)
InChIKeyIPFXNYPSBSIFOB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)CCOP(=O)(O)OP(=O)(O)O
CACTVS 3.341CC(C)CCO[P@](O)(=O)O[P](O)(O)=O
CACTVS 3.341CC(C)CCO[P](O)(=O)O[P](O)(O)=O
ACDLabs 10.04O=P(OP(=O)(O)O)(OCCC(C)C)O
OpenEye OEToolkits 1.5.0CC(C)CCO[P@@](=O)(O)OP(=O)(O)O
FormulaC5 H14 O7 P2
NameISOPENTYL PYROPHOSPHATE
ChEMBL
DrugBankDB02508
ZINCZINC000002579357
PDB chain3dyf Chain A Residue 6001 [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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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)		G46 K47 R50 Q96 R113 F251 D255
Binding residue
(residue number reindexed from 1)		G46 K47 R50 Q86 R103 F241 D245
Annotation score3
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 H88 D93 D97 R102 D165 K202 F241 D245 D246
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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