Structure of PDB 4k10 Chain A Binding Site BS02

Receptor Information
>4k10 Chain A (length=358) Species: 5664 (Leishmania major) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MAHMERFQKVYEEVQEFLLGDAEKRFEMDVHRKGYLKSMMDTTCLGGKYN
RGLCVVDVAEAMAKDTQMDAAAMERVLHDACVCGWMIEMLQAHFLVEDDI
MDHSKTRRGKPCWYLHPGVTAQVAINDGLILLAWATQMALHYFADRPFLA
EVLRVFHDVDLTTTIGQLYDVTSMVDSAKLDAKVAHANTTDYVEYTPFNH
RRIVVYKTAYYTYWLPLVMGLLVSGTLEKVDKKATHKVAMVMGEYFQVQD
DVMDCFTPPEKIGTDIEDAKCSWLAVTFLTTAPAEKVAEFKANYGSTDPA
AVAVIKQLYTEQNLLARFEEYEKAVVAEVEQLIAALEAQNAAFAASVKVL
WSKTYKRQ
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 chain4k10 Chain A Residue 406 [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]
PDB4k10 Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		D98 Q167 K207
Binding residue
(residue number reindexed from 1)		D98 Q167 K207
Annotation score1
Binding affinityMOAD: Kd=119.5nM
PDBbind-CN: -logKd/Ki=6.92,Kd=119.5nM
Enzymatic activity
Catalytic site (original residue number in PDB) K48 H93 D98 D102 R107 D170 K207 F246 D250 D251
Catalytic site (residue number reindexed from 1) K48 H93 D98 D102 R107 D170 K207 F246 D250 D251
Enzyme Commision number 2.5.1.1: dimethylallyltranstransferase.
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4k10, PDBe:4k10, PDBj:4k10
PDBsum4k10
PubMed24598749
UniProtQ4QBL1

[Back to BioLiP]