Structure of PDB 4dpt Chain B Binding Site BS02

Receptor Information
>4dpt Chain B (length=322) Species: 1282 (Staphylococcus epidermidis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVTFDP
DFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYVPTA
AGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFA
EWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNVSSRSGMSLTRDTSRF
YQYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFT
YLVQESYDAMAIVEQCRKANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFL
KVFDESKIIASDIISSGVEIIK
Ligand information
Ligand IDAGS
InChIInChI=1S/C10H16N5O12P3S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(25-10)1-24-28(18,19)26-29(20,21)27-30(22,23)31/h2-4,6-7,10,16-17H,1H2,(H,18,19)(H,20,21)(H2,11,12,13)(H2,22,23,31)/t4-,6-,7-,10-/m1/s1
InChIKeyNLTUCYMLOPLUHL-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[C@@H](O)[C@H]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=S)[CH](O)[CH]3O
OpenEye OEToolkits 1.7.6c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OP(=S)(O)O)O)O)N
ACDLabs 12.01O=P(O)(OP(=S)(O)O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
FormulaC10 H16 N5 O12 P3 S
NamePHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER;
ATP-GAMMA-S;
ADENOSINE 5'-(3-THIOTRIPHOSPHATE);
ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);
ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE
ChEMBLCHEMBL131890
DrugBankDB02930
ZINCZINC000008295128
PDB chain4dpt Chain B Residue 402 [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]
PDB4dpt Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase.
Resolution2.191 Å
Binding residue
(original residue number in PDB)		L60 E69 S94 N96 A101 A105 S106 S107 A108 A110 S192
Binding residue
(residue number reindexed from 1)		L59 E68 S93 N95 A100 A104 S105 S106 A107 A109 S187
Annotation score4
Enzymatic activity
Enzyme Commision number 4.1.1.33: diphosphomevalonate decarboxylase.
Gene Ontology
Molecular Function
GO:0004163 diphosphomevalonate decarboxylase activity
GO:0005524 ATP binding
GO:0016301 kinase activity
GO:0016829 lyase activity
GO:0016831 carboxy-lyase activity
Biological Process
GO:0006629 lipid metabolic process
GO:0008299 isoprenoid biosynthetic process
GO:0016310 phosphorylation
GO:0019287 isopentenyl diphosphate biosynthetic process, mevalonate pathway
Cellular Component
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4dpt, PDBe:4dpt, PDBj:4dpt
PDBsum4dpt
PubMed22734632
UniProtQ9FD73

[Back to BioLiP]