Structure of PDB 2z52 Chain A Binding Site BS03

Receptor Information
>2z52 Chain A (length=296) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
NKMEAKIDELINNDPVWSSQNESLISKPYNHILLKPLNLIVQINRVMNLP
KDQLAIVSQIVELLHNSSLLIDDIEDNAPLRRGQTTSHLIFGVPSTINTA
NYMYFRAMQLVSQLTTKEPLYHNLITIFNEELINLHRGQGLDIYWRDFLP
EIIPTQEMYLNMVMNKTGGLFRLTLRLMEALSPSHGHSLVPFINLLGIIY
QIRDDYLNLKDFQFAEDITEGKLSFPIVHALNFTKTKGQTEQHNEILRIL
LLRTSDKDIKLKLIQILEFDTNSLAYTKNFINQLVNMIKNDNKYLP
Ligand information
Ligand IDH23
InChIInChI=1S/C12H28O7P2/c1-2-3-4-5-6-7-8-9-10-11-12(13,20(14,15)16)21(17,18)19/h13H,2-11H2,1H3,(H2,14,15,16)(H2,17,18,19)
InChIKeyKKVZONPEMODBBG-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCCCCCCCCCC(O)(P(=O)(O)O)P(=O)(O)O
ACDLabs 10.04O=P(O)(O)C(O)(CCCCCCCCCCC)P(=O)(O)O
CACTVS 3.341CCCCCCCCCCCC(O)([P](O)(O)=O)[P](O)(O)=O
FormulaC12 H28 O7 P2
Name(1-HYDROXYDODECANE-1,1-DIYL)BIS(PHOSPHONIC ACID)
ChEMBLCHEMBL416301
DrugBankDB07873
ZINC
PDB chain2z52 Chain A Residue 1001 [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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PDB2z52 Inhibition of geranylgeranyl diphosphate synthase by bisphosphonates: a crystallographic and computational investigation
Resolution2.13 Å
Binding residue
(original residue number in PDB)		S76 D80 R89 Y112 L140 H144 Q147 K174 K238
Binding residue
(residue number reindexed from 1)		S68 D72 R81 Y104 L132 H136 Q139 K166 K222
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.57,IC50=2.69uM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2z52, PDBe:2z52, PDBj:2z52
PDBsum2z52
PubMed18800762
UniProtQ12051|GGPPS_YEAST Geranylgeranyl pyrophosphate synthase BTS1 (Gene Name=BTS1)

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