Structure of PDB 6rxq Chain A Binding Site BS03

Receptor Information
>6rxq Chain A (length=224) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KPRVLVLTGAGISAESGIRTFRAADGLWEEHRVEDVGTPEGFDRDPELVQ
AFYNARRRQLQQPEIQPNAAHLALAKLQDALGDRFLLVTQNCDNLHERAG
NTNVIHMHGELLKVRCSQSGQALDWTGDVTPPLRPHVVWFGEMPLGMDEI
YMALSMADIFIAIGTSGHVYPAAGFVHEAKLHGAHTVELNLEPSQVGNEF
AEKYYGPASQVVPEFVEKLLKGLK
Ligand information
Ligand IDKMQ
InChIInChI=1S/C19H29N5O14P2/c1-2-3-4-33-15-13(26)10(37-19(15)28)6-35-40(31,32)38-39(29,30)34-5-9-12(25)14(27)18(36-9)24-8-23-11-16(20)21-7-22-17(11)24/h2-3,7-10,12-15,18-19,25-28H,4-6H2,1H3,(H,29,30)(H,31,32)(H2,20,21,22)/b3-2+/t9-,10-,12-,13-,14-,15-,18-,19+/m1/s1
InChIKeyJOKNWQJJLFYBKK-YVAUJSGTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC=CCOC1C(C(OC1O)COP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)n3cnc4c3ncnc4N)O)O)O
OpenEye OEToolkits 2.0.7C/C=C/CO[C@@H]1[C@@H]([C@H](O[C@@H]1O)COP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)n3cnc4c3ncnc4N)O)O)O
CACTVS 3.385CC=CCO[CH]1[CH](O)O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)n3cnc4c(N)ncnc34)[CH]1O
CACTVS 3.385C\C=C\CO[C@H]1[C@@H](O)O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)n3cnc4c(N)ncnc34)[C@H]1O
FormulaC19 H29 N5 O14 P2
Name[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S})-4-[(~{E})-but-2-enoxy]-3,5-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain6rxq Chain E Residue 101 [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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PDB6rxq Evolved, Selective Erasers of Distinct Lysine Acylations.
Resolution1.7 Å
Binding residue
(original residue number in PDB)
G48 A49 G50 A53 E54 F60 Q129 H147 V188 G214 T215 S216 V219 N240 L241 P257 A258
Binding residue
(residue number reindexed from 1)
G9 A10 G11 A14 E15 F21 Q90 H108 V138 G164 T165 S166 V169 N190 L191 P207 A208
Annotation score3
Enzymatic activity
Enzyme Commision number 2.3.1.286: protein acetyllysine N-acetyltransferase.
Gene Ontology
Molecular Function
GO:0036054 protein-malonyllysine demalonylase activity
GO:0036055 protein-succinyllysine desuccinylase activity
GO:0070403 NAD+ binding

View graph for
Molecular Function
External links
PDB RCSB:6rxq, PDBe:6rxq, PDBj:6rxq
PDBsum6rxq
PubMed32187803
UniProtP75960|NPD_ECOLI NAD-dependent protein deacylase (Gene Name=cobB)

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