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Structure of PDB 9b71 Chain B Binding Site BS01

Receptor Information >9b71 Chain B (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 ID A1AI2 InChI InChI=1S/C46H75N9O13/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-17-32(56)53-30(16-15-23-50-45(48)49)41(62)52-27-29-20-18-28(19-21-29)26-51-34(43(63)64)39(68-44-38(61)35(58)31(25-47)66-44)40-36(59)37(60)42(67-40)55-24-22-33(57)54-46(55)65/h18-22,24,30-31,34-40,42,44,51,58-61H,2-17,23,25-27,47H2,1H3,(H,52,62)(H,53,56)(H,63,64)(H4,48,49,50)(H,54,57,65)/t30-,31+,34-,35+,36-,37+,38+,39-,40-,42+,44-/m0/s1 InChIKey GXLIRXIWCOLNIY-DZHYAEAPSA-N SMILES Software SMILES CACTVS 3.385 CCCCCCCCCCCCCCCC(=O)N[CH](CCCNC(N)=N)C(=O)NCc1ccc(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)cc1 OpenEye OEToolkits 2.0.7 [H]/N=C(\N)/NCCC[C@@H](C(=O)NCc1ccc(cc1)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)NC(=O)CCCCCCCCCCCCCCC CACTVS 3.385 CCCCCCCCCCCCCCCC(=O)N[C@@H](CCCNC(N)=N)C(=O)NCc1ccc(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)cc1 ACDLabs 12.01 N=C(N)NCCCC(NC(=O)CCCCCCCCCCCCCCC)C(=O)NCc1ccc(cc1)CNC(C(OC1OC(CN)C(O)C1O)C1OC(N2C=CC(=O)NC2=O)C(O)C1O)C(=O)O OpenEye OEToolkits 2.0.7 CCCCCCCCCCCCCCCC(=O)NC(CCCNC(=N)N)C(=O)NCc1ccc(cc1)CNC(C(C2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)OC4C(C(C(O4)CN)O)O)C(=O)O Formula C46 H75 N9 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-3-[(2~{S},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]-2-[[4-[[[(2~{S})-5-carbamimidamido-2-(hexadecanoylamino)pentanoyl]amino]methyl]phenyl]methylamino]propanoic acid ChEMBL DrugBank ZINC PDB chain 9b71 Chain B Residue 601 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]

Receptor-Ligand Complex Structure Global view Local view Structure 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] PDB 9b71 Development of a natural product optimization strategy for inhibitors against MraY, a promising antibacterial target. Resolution 2.7 Å Binding residue (original residue number in PDB) K70 I130 N190 L191 D193 G194 L195 D196 F262 G264 Binding residue (residue number reindexed from 1) K53 I113 N173 L174 D176 G177 L178 D179 F245 G247 Annotation score 1

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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