Structure of PDB 5dro Chain A Binding Site BS02

Receptor Information
>5dro Chain A (length=267) Species: 224324 (Aquifex aeolicus VF5) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GLEKTVKEKLSFEGVGIHTGEYSKLIIHPEKEGTGIRFFKNGVYIPARHE
FVVHTNHSTDLGFKGQRIKTVEHILSVLHLLEITNVTIEVIGNEIPILDG
SGWEFYEAIRKNILNQNREIDYFVVEEPIIVEDEGRLIKAEPSDTLEVTY
EGEFKNFLGRQKFTFVEGNEEEIVLARTFAFDWEIEHIKKVGLGKGGSLK
NTLVLGKDKVYNPEGLRYENEPVRHKVFDLIGDLYLLGSPVKGKFYSFRG
GHSLNVKLVKELAKKQK
Ligand information
Ligand IDZH2
InChIInChI=1S/C21H19N3O4/c1-14(25)19(21(27)24-28)23-20(26)17-10-6-15(7-11-17)4-2-3-5-16-8-12-18(22)13-9-16/h6-14,19,25,28H,22H2,1H3,(H,23,26)(H,24,27)/t14-,19+/m1/s1
InChIKeySNVYDNOGPYZQEV-KUHUBIRLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH](O)[CH](NC(=O)c1ccc(cc1)C#CC#Cc2ccc(N)cc2)C(=O)NO
OpenEye OEToolkits 1.7.6C[C@H]([C@@H](C(=O)NO)NC(=O)c1ccc(cc1)C#CC#Cc2ccc(cc2)N)O
CACTVS 3.385C[C@@H](O)[C@H](NC(=O)c1ccc(cc1)C#CC#Cc2ccc(N)cc2)C(=O)NO
ACDLabs 12.01c2c(C(NC(C(O)C)C(=O)NO)=O)ccc(C#CC#Cc1ccc(cc1)N)c2
OpenEye OEToolkits 1.7.6CC(C(C(=O)NO)NC(=O)c1ccc(cc1)C#CC#Cc2ccc(cc2)N)O
FormulaC21 H19 N3 O4
Name4-[4-(4-aminophenyl)buta-1,3-diyn-1-yl]-N-[(2S,3R)-3-hydroxy-1-(hydroxyamino)-1-oxobutan-2-yl]benzamide
ChEMBLCHEMBL1643369
DrugBank
ZINCZINC000066112219
PDB chain5dro Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5dro Drug design from the cryptic inhibitor envelope.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		H58 E73 H74 T179 F180 A181 G198 H226 D230 H253
Binding residue
(residue number reindexed from 1)		H57 E72 H73 T178 F179 A180 G197 H225 D229 H252
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=10.59,Ki=26pM
Enzymatic activity
Enzyme Commision number 3.5.1.108: UDP-3-O-acyl-N-acetylglucosamine deacetylase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0103117 UDP-3-O-acyl-N-acetylglucosamine deacetylase activity
Biological Process
GO:0006796 phosphate-containing compound metabolic process
GO:0009245 lipid A biosynthetic process
GO:0019637 organophosphate metabolic process
GO:1901135 carbohydrate derivative metabolic process

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Molecular Function
View graph for
Biological Process
External links
PDB RCSB:5dro, PDBe:5dro, PDBj:5dro
PDBsum5dro
PubMed26912110
UniProtO67648|LPXC_AQUAE UDP-3-O-acyl-N-acetylglucosamine deacetylase (Gene Name=lpxC)

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