Structure of PDB 4jzb Chain A Binding Site BS04

Receptor Information
>4jzb Chain A (length=362) 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
DVMDCFTPPEKLGKIGTDIEDAKCSWLAVTFLTTAPAEKVAEFKANYGST
DPAAVAVIKQLYTEQNLLARFEEYEKAVVAEVEQLIAALEAQNAAFAASV
KVLWSKTYKRQK
Ligand information
Ligand IDP2H
InChIInChI=1S/C13H15NO7P2/c15-13(22(16,17)18,23(19,20)21)10-14-8-4-7-12(9-14)11-5-2-1-3-6-11/h1-9,15H,10H2,(H3-,16,17,18,19,20,21)/p+1
InChIKeyZYEONEYSNIUGRA-UHFFFAOYSA-O
SMILES
SoftwareSMILES
ACDLabs 11.02O=P(O)(O)C(O)(P(=O)(O)O)C[n+]2cccc(c1ccccc1)c2
CACTVS 3.352OC(C[n+]1cccc(c1)c2ccccc2)([P](O)(O)=O)[P](O)(O)=O
OpenEye OEToolkits 1.7.0c1ccc(cc1)c2ccc[n+](c2)CC(O)(P(=O)(O)O)P(=O)(O)O
FormulaC13 H16 N O7 P2
Name1-(2-hydroxy-2,2-diphosphonoethyl)-3-phenylpyridinium
ChEMBLCHEMBL196726
DrugBank
ZINCZINC000013643025
PDB chain4jzb Chain A Residue 405 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jzb Structural and thermodynamic basis of the inhibition of Leishmania major farnesyl diphosphate synthase by nitrogen-containing bisphosphonates.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		F94 D98 R107 T163 Q167 K207 D250 K264
Binding residue
(residue number reindexed from 1)		F94 D98 R107 T163 Q167 K207 D250 K264
Annotation score1
Binding affinityMOAD: Kd=342.5nM
PDBbind-CN: -logKd/Ki=6.47,Kd=342.5nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4jzb, PDBe:4jzb, PDBj:4jzb
PDBsum4jzb
PubMed24598749
UniProtQ4QBL1

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