Structure of PDB 6oyh Chain D Binding Site BS01

Receptor Information
>6oyh Chain D (length=337) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AFNVLKYITFRSFTAVLIAFFLTLVLSPSFINRLRKIQRVREYTPHEVKK
YTPTMGGIVILIVVTLSTLLLMRWDIKYTWVVLLSFLSFGTIGFWDDYVK
LKNKKGISIKTKFLLQVLSASLISVLIYYWADIDTILYFPFFKELYVDLG
VLYLPFAVFVIVGSANAVNLTDGLDGLAIGPAMTTATALGVVAYAVGHSK
IAQYLNIPYVPYAGELTVFCFALVGAGLGFLWFNSFPAQMFMGDVGSLSI
GASLATVALLTKSEFIFAVAAGVFVFETISVILQIIYFRWTGGKRLFKRA
PFHHHLELNGLPEPKIVVRMWIISILLAIIAISMLKL
Ligand information
Ligand IDNK4
InChIInChI=1S/C39H67N5O12/c1-4-5-6-7-8-9-10-11-12-13-14-15-16-17-18-19-24-23-42(2)28(35(50)43(3)27(24)37(51)52)33(56-38-32(49)29(46)25(22-40)54-38)34-30(47)31(48)36(55-34)44-21-20-26(45)41-39(44)53/h20-21,24-25,27-34,36,38,46-49H,4-19,22-23,40H2,1-3H3,(H,51,52)(H,41,45,53)/t24-,25+,27-,28-,29+,30-,31+,32+,33-,34-,36+,38-/m0/s1
InChIKeyGERCPLXZNIROKC-PUWYXTMPSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01C1(CN)C(C(O)C(O1)OC(C2N(CC(CCCCCCCCCCCCCCCCC)C(C(O)=O)N(C)C2=O)C)C4C(C(C(N3C(NC(C=C3)=O)=O)O4)O)O)O
CACTVS 3.385CCCCCCCCCCCCCCCCC[CH]1CN(C)[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)N(C)[CH]1C(O)=O
CACTVS 3.385CCCCCCCCCCCCCCCCC[C@H]1CN(C)[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)N(C)[C@@H]1C(O)=O
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCCCCC[C@H]1CN([C@H](C(=O)N([C@@H]1C(=O)O)C)[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
OpenEye OEToolkits 2.0.7CCCCCCCCCCCCCCCCCC1CN(C(C(=O)N(C1C(=O)O)C)C(C2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)OC4C(C(C(O4)CN)O)O)C
FormulaC39 H67 N5 O12
Name(5S)-5'-O-(5-amino-5-deoxy-beta-D-ribofuranosyl)-5'-C-[(2S,5S,6S)-5-carboxy-6-heptadecyl-1,4-dimethyl-3-oxo-1,4-diazepan-2-yl]uridine
ChEMBLCHEMBL4466734
DrugBank
ZINC
PDB chain6oyh Chain D 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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PDB6oyh Chemical logic of MraY inhibition by antibacterial nucleoside natural products.
Resolution2.95 Å
Binding residue
(original residue number in PDB)		K70 N190 D193 G194 L195 D196 F262 M263 G264 P322 H324 H325
Binding residue
(residue number reindexed from 1)		K49 N169 D172 G173 L174 D175 F241 M242 G243 P301 H303 H304
Annotation score1
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:6oyh, PDBe:6oyh, PDBj:6oyh
PDBsum6oyh
PubMed31266949
UniProtO66465|MRAY_AQUAE Phospho-N-acetylmuramoyl-pentapeptide-transferase (Gene Name=mraY)

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