Structure of PDB 9b70 Chain A Binding Site BS01

Receptor Information
>9b70 Chain A (length=341) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VLKYITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRLFGGYVREYTPESH
EVKKYTPTMGGIVILIVVTLSTLLLMRWDIKYTWVVLLSFLSFGTIGFWD
DYVKLKNKKGISIKTKFLLQVLSASLISVLIYYWADIDTILYFPFFKELY
VDLGVLYLPFAVFVIVGSANAVNLTDGLDGLAIGPAMTTATALGVVAYAV
GHSKIAQYLNIPYVPYAGELTVFCFALVGAGLGFLWFNSFPAQMFMGDVG
SLSIGASLATVALLTKSEFIFAVAAGVFVFETISVILQIIYFRWTGGKRL
FKRAPFHHHLELNGLPEPKIVVRMWIISILLAIIAISMLKL
Ligand information
Ligand IDA1AI1
InChIInChI=1S/C46H75N7O13/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-21-33(54)51-31(20-15-16-23-47)42(60)50-28-30-19-17-18-29(25-30)27-49-35(44(61)62)40(66-45-39(59)36(56)32(26-48)64-45)41-37(57)38(58)43(65-41)53-24-22-34(55)52-46(53)63/h17-19,22,24-25,31-32,35-41,43,45,49,56-59H,2-16,20-21,23,26-28,47-48H2,1H3,(H,50,60)(H,51,54)(H,61,62)(H,52,55,63)/t31-,32+,35-,36+,37-,38+,39+,40-,41-,43+,45-/m0/s1
InChIKeyQOXTVOOYHAUVQY-YCVAMTARSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CCCCCCCCCCCCCCCC(=O)N[CH](CCCCN)C(=O)NCc1cccc(CN[CH]([CH](O[CH]2O[CH](CN)[CH](O)[CH]2O)[CH]3O[CH]([CH](O)[CH]3O)N4C=CC(=O)NC4=O)C(O)=O)c1
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCCCC(=O)N[C@@H](CCCCN)C(=O)NCc1cccc(c1)CN[C@@H]([C@@H]([C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)O[C@H]4[C@@H]([C@@H]([C@H](O4)CN)O)O)C(=O)O
CACTVS 3.385CCCCCCCCCCCCCCCC(=O)N[C@@H](CCCCN)C(=O)NCc1cccc(CN[C@@H]([C@H](O[C@@H]2O[C@H](CN)[C@@H](O)[C@H]2O)[C@H]3O[C@H]([C@H](O)[C@@H]3O)N4C=CC(=O)NC4=O)C(O)=O)c1
ACDLabs 12.01CCCCCCCCCCCCCCCC(=O)NC(CCCCN)C(=O)NCc1cccc(c1)CNC(C(OC1OC(CN)C(O)C1O)C1OC(N2C=CC(=O)NC2=O)C(O)C1O)C(=O)O
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCCCC(=O)NC(CCCCN)C(=O)NCc1cccc(c1)CNC(C(C2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)OC4C(C(C(O4)CN)O)O)C(=O)O
FormulaC46 H75 N7 O13
Name(2~{S},3~{S})-3-[(2~{S},3~{R},4~{S},5~{R})-5-(aminomethyl)-3,4-bis(oxidanyl)oxolan-2-yl]oxy-2-[[3-[[[(2~{S})-6-azanyl-2-(hexadecanoylamino)hexanoyl]amino]methyl]phenyl]methylamino]-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]propanoic acid
ChEMBL
DrugBank
ZINC
PDB chain9b70 Chain A Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB9b70 Development of a natural product optimization strategy for inhibitors against MraY, a promising antibacterial target.
Resolution2.88 Å
Binding residue
(original residue number in PDB)
K70 N190 D193 G194 L195 D196 F262 G264 T299
Binding residue
(residue number reindexed from 1)
K53 N173 D176 G177 L178 D179 F245 G247 T282
Annotation score1
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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:9b70, PDBe:9b70, PDBj:9b70
PDBsum9b70
PubMed38877016
UniProtO66465|MRAY_AQUAE Phospho-N-acetylmuramoyl-pentapeptide-transferase (Gene Name=mraY)

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