Structure of PDB 4dpy Chain B Binding Site BS01

Receptor Information
>4dpy Chain B (length=321) Species: 1282 (Staphylococcus epidermidis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VKSGKARAHTNIALIKYWGKADETYIIPMNNSLSVTLDRFYTETKVTFDP
DFTEDCLILNGNEVNAKEKEKIQNYMNIVRDLAGNRLHARIESENYVPTA
AGLASSASAYAALAAACNEALSLNLSDTDLSRLARRGSGSASRSIFGGFA
EWEKGHDDLTSYAHGINSNGWEKDLSMIFVVINNVSARSGMSLTRDTSRF
YQYWLDHVDEDLNEAKEAVKNQDFQRLGEVIEANGLRMHATNLGAQPPFT
YLVQESYDAMAIVEQCRKANLPCYFTMDAGPNVKVLVEKKNKQAVMEQFL
KVFDESKIIASDIISSGVEII
Ligand information
Ligand ID2P0
InChIInChI=1S/C7H13NO10P2/c9-6(8-3-1-2-5(8)7(10)11)4-17-20(15,16)18-19(12,13)14/h5H,1-4H2,(H,10,11)(H,15,16)(H2,12,13,14)/t5-/m0/s1
InChIKeyJFTJDUMMWOSHFL-YFKPBYRVSA-N
SMILES
SoftwareSMILES
CACTVS 3.370OC(=O)[C@@H]1CCCN1C(=O)CO[P](O)(=O)O[P](O)(O)=O
OpenEye OEToolkits 1.7.0C1CC(N(C1)C(=O)COP(=O)(O)OP(=O)(O)O)C(=O)O
ACDLabs 12.01O=C(N1C(C(=O)O)CCC1)COP(=O)(O)OP(=O)(O)O
OpenEye OEToolkits 1.7.0C1C[C@H](N(C1)C(=O)CO[P@](=O)(O)OP(=O)(O)O)C(=O)O
CACTVS 3.370OC(=O)[CH]1CCCN1C(=O)CO[P](O)(=O)O[P](O)(O)=O
FormulaC7 H13 N O10 P2
Name1-({[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}acetyl)-L-proline;
diphosphoglycolylproline
ChEMBLCHEMBL1160294
DrugBank
ZINCZINC000095539351
PDB chain4dpy Chain B Residue 401 [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]
PDB4dpy Structural basis for nucleotide binding and reaction catalysis in mevalonate diphosphate decarboxylase.
Resolution2.14 Å
Binding residue
(original residue number in PDB)		A14 Y18 K21 S107 S139 G140 S141 R144 A192 R193 D283
Binding residue
(residue number reindexed from 1)		A13 Y17 K20 S106 S138 G139 S140 R143 A187 R188 D278
Annotation score1
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:4dpy, PDBe:4dpy, PDBj:4dpy
PDBsum4dpy
PubMed22734632
UniProtQ9FD73

[Back to BioLiP]