Structure of PDB 2z78 Chain A Binding Site BS01

Receptor Information
>2z78 Chain A (length=321) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NKMEAKIDELINNDPVWSSQNESLISKPYNHILLKPGKNFRLNLIVQINR
VMNLPKDQLAIVSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPS
TINTANYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYW
RDFLPEIIPTQEMYLNMVMNKTGGLFRLTLRLMEALSPSSHHGHSLVPFI
NLLGIIYQIRDDYLNLKDFQMSKGFAEDITEGKLSFPIVHALNFTKTKGQ
TEQHNEILRILLLRTSDKDIKLKLIQILEFDTNSLAYTKNFINQLVNMIK
NDNENKYLPELLYIIDHLSEL
Ligand information
Ligand IDH86
InChIInChI=1S/C23H33F2NO7P2/c1-2-3-4-5-6-7-8-9-10-33-22-13-19(18-11-20(24)14-21(25)12-18)15-26(16-22)17-23(34(27,28)29)35(30,31)32/h11-16,23H,2-10,17H2,1H3,(H3-,27,28,29,30,31,32)/p+1
InChIKeyJONDYIHZOFRLBH-UHFFFAOYSA-O
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCCCCOc1cc(c[n+](CC([P](O)(O)=O)[P](O)(O)=O)c1)c2cc(F)cc(F)c2
ACDLabs 10.04O=P(O)(O)C(P(=O)(O)O)C[n+]1cc(cc(OCCCCCCCCCC)c1)c2cc(F)cc(F)c2
OpenEye OEToolkits 1.5.0CCCCCCCCCCOc1cc(c[n+](c1)CC(P(=O)(O)O)P(=O)(O)O)c2cc(cc(c2)F)F
FormulaC23 H34 F2 N O7 P2
Name3-(decyloxy)-5-(3,5-difluorophenyl)-1-(2,2-diphosphonoethyl)pyridinium
ChEMBL
DrugBank
ZINCZINC000016052648
PDB chain2z78 Chain A Residue 1300 [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]
PDB2z78 Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation
Resolution2.1 Å
Binding residue
(original residue number in PDB)		I48 H73 S76 I79 D80 R89 L143 Q147 T175 F179 Y210 Q211 D214 K238
Binding residue
(residue number reindexed from 1)		I45 H70 S73 I76 D77 R86 L140 Q144 T172 F176 Y207 Q208 D211 K233
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.12,IC50=0.76uM
Enzymatic activity
Enzyme Commision number 2.5.1.-
2.5.1.1: dimethylallyltranstransferase.
2.5.1.10: (2E,6E)-farnesyl diphosphate synthase.
2.5.1.29: geranylgeranyl diphosphate synthase.
Gene Ontology
Molecular Function
GO:0004161 dimethylallyltranstransferase activity
GO:0004311 farnesyltranstransferase activity
GO:0004337 geranyltranstransferase activity
GO:0004659 prenyltransferase activity
GO:0016740 transferase activity
GO:0046872 metal ion binding
Biological Process
GO:0008299 isoprenoid biosynthetic process
GO:0015031 protein transport
GO:0016114 terpenoid biosynthetic process
GO:0033384 geranyl diphosphate biosynthetic process
GO:0033386 geranylgeranyl diphosphate biosynthetic process
GO:0045337 farnesyl diphosphate biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005739 mitochondrion

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:2z78, PDBe:2z78, PDBj:2z78
PDBsum2z78
PubMed18800762
UniProtQ12051|GGPPS_YEAST Geranylgeranyl pyrophosphate synthase BTS1 (Gene Name=BTS1)

[Back to BioLiP]