Structure of PDB 6p8a Chain A Binding Site BS01

Receptor Information
>6p8a Chain A (length=335) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SIRLADLAQQLDAELHGDGDIVITGVASMQSAQTGHITFMVNPKYREHLG
LCQASAVVMTQDDLPFAKSAALVVKNPYLTYARMAQILDTTPQPAQNIAP
SAVIDATAKLGNNVSIGANAVIESGVELGDNVIIGAGCFVGKNSKIGAGS
RLWANVTIYHEIQIGQNCLIQSGTVVGADGFGYANDRGNWVKIPQIGRVI
IGDRVEIGACTTIDRGALDDTIIGNGVIIDNQCQIAHNVVIGDNTAVAGG
VIMAGSLKIGRYCMIGGASVINGHMEICDKVTVTGMGMVMRPITEPGVYS
SGIPLQPNKVWRKTAALVMNIDDMSKRLKSLERKV
Ligand information
Ligand IDO4D
InChIInChI=1S/C21H28N6O2/c1-16-14-17(2)23-20-19(16)21(26-8-3-4-9-26)24-27(20)15-18(28)22-6-5-7-25-10-12-29-13-11-25/h3-4,8-9,14H,5-7,10-13,15H2,1-2H3,(H,22,28)
InChIKeyAZMBNAXBTVHIKQ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c2(c3c(n(CC(NCCCN1CCOCC1)=O)n2)nc(cc3C)C)n4cccc4
CACTVS 3.385Cc1cc(C)c2c(n1)n(CC(=O)NCCCN3CCOCC3)nc2n4cccc4
OpenEye OEToolkits 2.0.7Cc1cc(nc2c1c(nn2CC(=O)NCCCN3CCOCC3)n4cccc4)C
FormulaC21 H28 N6 O2
Name2-[4,6-dimethyl-3-(1H-pyrrol-1-yl)-1H-pyrazolo[3,4-b]pyridin-1-yl]-N-[3-(morpholin-4-yl)propyl]acetamide
ChEMBL
DrugBank
ZINCZINC000020992666
PDB chain6p8a Chain A Residue 403 [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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PDB6p8a Structural and Biological Basis of Small Molecule Inhibition ofEscherichia coliLpxD Acyltransferase Essential for Lipopolysaccharide Biosynthesis.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		A248 A250 M266 I267 G268 T286 G287
Binding residue
(residue number reindexed from 1)		A246 A248 M264 I265 G266 T284 G285
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=3.59,Kd=255uM
Enzymatic activity
Enzyme Commision number 2.3.1.191: UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase.
Gene Ontology
Molecular Function
GO:0005515 protein binding
GO:0016410 N-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
GO:0103118 UDP-3-O-(R-3-hydroxymyristoyl)-glucosamine N-acyltransferase activity
Biological Process
GO:0009245 lipid A biosynthetic process
GO:0046677 response to antibiotic
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:6p8a, PDBe:6p8a, PDBj:6p8a
PDBsum6p8a
PubMed31402665
UniProtP21645|LPXD_ECOLI UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase (Gene Name=lpxD)

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