Structure of PDB 6oyz Chain A Binding Site BS01

Receptor Information
>6oyz Chain A (length=313) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRKKYTPTMGGIVILIVVT
LSTLLLMRWDIKYTWVVLLSFLSFGTIGFWDDYVKLKNKKGISIKTKFLL
QVLSASLISVLIYYWADIDTILYFPFFKELYVDLGVLYLPFAVFVIVGSA
NAVNLTDGLDGLAIGPAMTTATALGVVAYAVGHSKIAQYLNIPYVPYAGE
LTVFCFALVGAGLGFLWFNSFPAQMFMGDVGSLSIGASLATVALLTKSEF
IFAVAAGVFVFETISVILQIIYFRWTPFHHHLELNGLPEPKIVVRMWIIS
ILLAIIAISMLKL
Ligand information
Ligand IDNKM
InChIInChI=1S/C23H31N5O12/c1-37-15-14(32)21(28-7-5-12(30)27-23(28)36)39-16(15)17(18(24)33)40-22-13(31)10(29)8-11(38-22)20(35)26-9-4-2-3-6-25-19(9)34/h5,7-10,13-17,21-22,29,31-32H,2-4,6H2,1H3,(H2,24,33)(H,25,34)(H,26,35)(H,27,30,36)/t9-,10-,13-,14+,15-,16-,17+,21+,22+/m0/s1
InChIKeyBISOEENGZHMDEO-RLXIHFJVSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COC1C(C(OC1C(C(=O)N)OC2C(C(C=C(O2)C(=O)NC3CCCCNC3=O)O)O)N4C=CC(=O)NC4=O)O
CACTVS 3.385CO[C@H]1[C@@H](O)[C@@H](O[C@@H]1[C@@H](O[C@H]2OC(=C[C@H](O)[C@@H]2O)C(=O)N[C@H]3CCCCNC3=O)C(N)=O)N4C=CC(=O)NC4=O
ACDLabs 12.01C1(OC(=CC(O)C1O)C(=O)NC2CCCCNC2=O)OC(C4C(C(C(N3C=CC(=O)NC3=O)O4)O)OC)C(=O)N
OpenEye OEToolkits 2.0.7CO[C@H]1[C@H]([C@@H](O[C@@H]1[C@H](C(=O)N)O[C@@H]2[C@H]([C@H](C=C(O2)C(=O)N[C@H]3CCCCNC3=O)O)O)N4C=CC(=O)NC4=O)O
CACTVS 3.385CO[CH]1[CH](O)[CH](O[CH]1[CH](O[CH]2OC(=C[CH](O)[CH]2O)C(=O)N[CH]3CCCCNC3=O)C(N)=O)N4C=CC(=O)NC4=O
FormulaC23 H31 N5 O12
Name(2~{S},3~{S},4~{S})-2-[(1~{R})-2-azanyl-1-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3-methoxy-4-oxidanyl-oxolan-2-yl]-2-oxidanylidene-ethoxy]-3,4-bis(oxidanyl)-~{N}-[(3~{S})-2-oxidanylideneazepan-3-yl]-3,4-dihydro-2~{H}-pyran-6-carboxamide
ChEMBLCHEMBL96695
DrugBank
ZINCZINC000026672118
PDB chain6oyz 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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PDB6oyz Chemical logic of MraY inhibition by antibacterial nucleoside natural products.
Resolution3.62 Å
Binding residue
(original residue number in PDB)		K70 T75 K121 D193 G194 L195 D196 F262 M263 G264
Binding residue
(residue number reindexed from 1)		K34 T39 K85 D157 G158 L159 D160 F226 M227 G228
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.73,IC50=185nM
Enzymatic activity
Enzyme Commision number 2.7.8.13: phospho-N-acetylmuramoyl-pentapeptide-transferase.
Gene Ontology
Molecular Function
GO:0008963 phospho-N-acetylmuramoyl-pentapeptide-transferase activity
GO:0016740 transferase activity
GO:0016780 phosphotransferase activity, for other substituted phosphate groups
GO:0042802 identical protein binding
GO:0046872 metal ion binding
GO:0051992 UDP-N-acetylmuramoyl-L-alanyl-D-glutamyl-meso-2,6-diaminopimelyl-D-alanyl-D-alanine:undecaprenyl-phosphate transferase activity
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0044038 cell wall macromolecule biosynthetic process
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005886 plasma membrane
GO:0016020 membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:6oyz, PDBe:6oyz, PDBj:6oyz
PDBsum6oyz
PubMed31266949
UniProtO66465|MRAY_AQUAE Phospho-N-acetylmuramoyl-pentapeptide-transferase (Gene Name=mraY)

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