Structure of PDB 5v2l Chain A Binding Site BS01

Receptor Information
>5v2l Chain A (length=321) Species: 226185 (Enterococcus faecalis V583) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AMLSGKARAHTNIALIKYWGKANEEYILPMNSSLSLTLDAFYTETTVTFD
AHYSEDVFILNGILQNEKQTKKVKEFLNLVRQQADCTWFAKVESQNFVPT
AAGLASSASGLAALAGACNVALGLNLSAKDLSRLARRGSGSACRSIFGGF
AQWNKGHSDETSFAENIPANNWENELAMLFILINSSRDGMKRTVETSSFY
QGWLDNVEKDLSQVHEAIKTKDFPRLGEIIEANGLRMHGTTLGAVPPFTY
WSPGSLQAMALVRQARAKGIPCYFTMDAGPNVKVLVEKKNLEALKTFLSE
HFSKEQLVPAFAGPGIELFET
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain5v2l Chain A Residue 401 [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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PDB5v2l Mevalonate 5-diphosphate mediates ATP binding to the mevalonate diphosphate decarboxylase from the bacterial pathogen Enterococcus faecalis.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		F57 V72 S93 N95 A104 G109
Binding residue
(residue number reindexed from 1)		F58 V73 S94 N96 A105 G110
Annotation score5
Binding affinityPDBbind-CN: -logKd/Ki=3.54,Kd=288uM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5v2l, PDBe:5v2l, PDBj:5v2l
PDBsum5v2l
PubMed29025876
UniProtQ837E0

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