Structure of PDB 5afx Chain B Binding Site BS04

Receptor Information
>5afx Chain B (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 IDPVZ
InChIInChI=1S/C14H28N2O7P2/c1-2-3-4-5-6-7-8-9-15-10-11-16(13-15)12-14(17,24(18,19)20)25(21,22)23/h10-11,13,17H,2-9,12H2,1H3,(H3-,18,19,20,21,22,23)/p+1
InChIKeyANVJZSKZYXLDSP-UHFFFAOYSA-O
SMILES
SoftwareSMILES
ACDLabs 12.01O=P(O)(O)C(O)(P(=O)(O)O)C[n+]1ccn(c1)CCCCCCCCC
CACTVS 3.385CCCCCCCCCn1cc[n+](CC(O)([P](O)(O)=O)[P](O)(O)=O)c1
OpenEye OEToolkits 1.7.6CCCCCCCCCn1cc[n+](c1)CC(O)(P(=O)(O)O)P(=O)(O)O
FormulaC14 H29 N2 O7 P2
Name[1-hydroxy-2-(1-nonyl-1H-3lambda~5~-imidazol-3-yl)ethane-1,1-diyl]bis(phosphonic acid)
ChEMBL
DrugBank
ZINCZINC000095591505
PDB chain5afx Chain B Residue 1371 [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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PDB5afx Inhibition of Trypanosoma Brucei Cell Growth by Lipophilic Bisphosphonates: An in Vitro and in Vivo Investigation.
Resolution2.39 Å
Binding residue
(original residue number in PDB)		Y99 D103 R112 T168 A169 Q172 K212 Y216 D255 K269
Binding residue
(residue number reindexed from 1)		Y89 D93 R102 T158 A159 Q162 K202 Y206 D245 K259
Annotation score1
Binding affinityMOAD: ic50=1.2uM
PDBbind-CN: -logKd/Ki=5.92,IC50=1.2uM
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 ?
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:5afx, PDBe:5afx, PDBj:5afx
PDBsum5afx
PubMed26392508
UniProtQ86C09

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