Structure of PDB 6p9t Chain A Binding Site BS01

Receptor Information
>6p9t Chain A (length=263) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIDKSAFVHPTAIVEEGASIGANAHIGPFCIVGPHVEIGEGTVLKSHVVV
NGHTKIGRDNEIYQFASIGEVNQDLKYAGEPTRVEIGDRNRIRESVTIHR
GTVQGGGLTKVGSDNLLMINAHIAHDCTVGNRCILANNATLAGHVSVDDF
AIIGGMTAVHQFCIIGAHVMVGGCSGVAQDVPPYVIAQGNHATPFGVNIE
GLKRRGFSREAITAIRNAYKLIYRSGKTLDEVKPEIAELAETYPEVKAFT
DFFARSTRGLIRH
Ligand information
Ligand IDU20
InChIInChI=1S/C31H53N3O19P2/c1-3-4-5-6-7-8-9-10-11-12-19(37)15-23(39)51-28-24(32-18(2)36)30(50-20(16-35)26(28)41)52-55(46,47)53-54(44,45)48-17-21-25(40)27(42)29(49-21)34-14-13-22(38)33-31(34)43/h13-14,19-21,24-30,35,37,40-42H,3-12,15-17H2,1-2H3,(H,32,36)(H,44,45)(H,46,47)(H,33,38,43)/t19-,20-,21-,24-,25-,26-,27-,28-,29-,30-/m1/s1
InChIKeyTZSJGZGYQDNRRX-MPLCHSTDSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCCCCC[CH](O)CC(=O)O[CH]1[CH](O)[CH](CO)O[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O)[CH]1NC(C)=O
OpenEye OEToolkits 1.5.0CCCCCCCCCCCC(CC(=O)OC1C(C(OC(C1O)CO)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C)O
OpenEye OEToolkits 1.5.0CCCCCCCCCCC[C@H](CC(=O)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)O[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)NC(=O)C)O
ACDLabs 10.04O=P(OC1OC(C(O)C(OC(=O)CC(O)CCCCCCCCCCC)C1NC(=O)C)CO)(O)OP(=O)(O)OCC3OC(N2C=CC(=O)NC2=O)C(O)C3O
CACTVS 3.341CCCCCCCCCCC[C@@H](O)CC(=O)O[C@H]1[C@H](O)[C@@H](CO)O[C@H](O[P@](O)(=O)O[P@](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O)[C@@H]1NC(C)=O
FormulaC31 H53 N3 O19 P2
Nameuridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-N-acetyl-D-glucosamine;
(2R,3R,4R,5S,6R)-3-(acetylamino)-2-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydrox ytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H- pyran-4-yl (3R)-3-hydroxytetradecanoate
ChEMBL
DrugBank
ZINCZINC000087520386
PDB chain6p9t Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6p9t Two Distinct Mechanisms of Inhibition of LpxA Acyltransferase Essential for Lipopolysaccharide Biosynthesis.
Resolution1.75 Å
Binding residue
(original residue number in PDB)
D74 L75 K76 H122 A124 H125 A142 G143 H144 A158 Q161
Binding residue
(residue number reindexed from 1)
D74 L75 K76 H122 A124 H125 A142 G143 H144 A158 Q161
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) H125 D126 G143
Catalytic site (residue number reindexed from 1) H125 D126 G143
Enzyme Commision number 2.3.1.129: acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase.
Gene Ontology
Molecular Function
GO:0008780 acyl-[acyl-carrier-protein]-UDP-N-acetylglucosamine O-acyltransferase activity
GO:0016740 transferase activity
GO:0016746 acyltransferase activity
GO:0016747 acyltransferase activity, transferring groups other than amino-acyl groups
GO:0042802 identical protein binding
Biological Process
GO:0008610 lipid biosynthetic process
GO:0009245 lipid A biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:6p9t, PDBe:6p9t, PDBj:6p9t
PDBsum6p9t
PubMed32064871
UniProtP0A722|LPXA_ECOLI Acyl-[acyl-carrier-protein]--UDP-N-acetylglucosamine O-acyltransferase (Gene Name=lpxA)

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