Structure of PDB 4yq4 Chain A Binding Site BS01

Receptor Information
>4yq4 Chain A (length=242) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHK
TVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQG
GVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMT
LIDAVARFIPGVLGDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEI
RKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Ligand information
Ligand ID4G3
InChIInChI=1S/C13H13N3O2/c14-13(18)10-4-5-12(16-8-10)15-7-9-2-1-3-11(17)6-9/h1-6,8,17H,7H2,(H2,14,18)(H,15,16)
InChIKeyWNJXCRUMIMMAQO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC(=O)c1ccc(NCc2cccc(O)c2)nc1
ACDLabs 12.01
OpenEye OEToolkits 1.9.2		c1cc(cc(c1)O)CNc2ccc(cn2)C(=O)N
FormulaC13 H13 N3 O2
Name6-[(3-hydroxybenzyl)amino]pyridine-3-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain4yq4 Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4yq4 Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Resolution1.89 Å
Binding residue
(original residue number in PDB)		Y86 L87 S88 P89 G117 S132 I133 Y136 L138 G140 P144
Binding residue
(residue number reindexed from 1)		Y89 L90 S91 P92 G120 S135 I136 Y139 L141 G143 P147
Annotation score1
Binding affinityBindingDB: IC50=1995nM
Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154 D169
Catalytic site (residue number reindexed from 1) P92 E119 R157 D165
Enzyme Commision number 2.1.1.228: tRNA (guanine(37)-N(1))-methyltransferase.
Gene Ontology
Molecular Function
GO:0008168 methyltransferase activity
GO:0052906 tRNA (guanine(37)-N1)-methyltransferase activity
Biological Process
GO:0002939 tRNA N1-guanine methylation
GO:0006400 tRNA modification
GO:0008033 tRNA processing
GO:0032259 methylation
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4yq4, PDBe:4yq4, PDBj:4yq4
PDBsum4yq4
PubMed
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

[Back to BioLiP]