Structure of PDB 4rxe Chain B Binding Site BS01

Receptor Information
>4rxe 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 ID3YQ
InChIInChI=1S/C7H12N2O6P2/c1-5-3-2-4-8-6(5)9-7(16(10,11)12)17(13,14)15/h2-4,7H,1H3,(H,8,9)(H2,10,11,12)(H2,13,14,15)
InChIKeyNAIJOBGUXRHQJW-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1cccnc1NC([P](O)(O)=O)[P](O)(O)=O
ACDLabs 12.01O=P(O)(O)C(Nc1ncccc1C)P(=O)(O)O
OpenEye OEToolkits 1.7.6Cc1cccnc1NC(P(=O)(O)O)P(=O)(O)O
FormulaC7 H12 N2 O6 P2
Name{[(3-methylpyridin-2-yl)amino]methanediyl}bis(phosphonic acid)
ChEMBLCHEMBL55140
DrugBank
ZINCZINC000013473668
PDB chain4rxe Chain B Residue 4001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4rxe Farnesyl diphosphate synthase inhibitors with unique ligand-binding geometries.
Resolution2.5 Å
Binding residue
(original residue number in PDB)		L100 D103 R112 K212 Y216 D255
Binding residue
(residue number reindexed from 1)		L92 D95 R104 K204 Y208 D247
Annotation score1
Binding affinityMOAD: ic50=230nM
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 ?
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4rxe, PDBe:4rxe, PDBj:4rxe
PDBsum4rxe
PubMed25815158
UniProtQ86C09

[Back to BioLiP]