Structure of PDB 4yq7 Chain A Binding Site BS01

Receptor Information
>4yq7 Chain A (length=238) 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
LIDAVARFIPGVLGDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWR
LKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Ligand information
Ligand ID4G4
InChIInChI=1S/C15H18N4O/c1-19(2)13-6-4-3-5-11(13)9-17-14-8-7-12(10-18-14)15(16)20/h3-8,10H,9H2,1-2H3,(H2,16,20)(H,17,18)
InChIKeyOQZMUCDXSPWFIT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2CN(C)c1ccccc1CNc2ccc(cn2)C(=O)N
ACDLabs 12.01c2cc(CNc1ccc(cn1)C(=O)N)c(cc2)N(C)C
CACTVS 3.385CN(C)c1ccccc1CNc2ccc(cn2)C(N)=O
FormulaC15 H18 N4 O
Name6-{[2-(dimethylamino)benzyl]amino}pyridine-3-carboxamide
ChEMBL
DrugBank
ZINCZINC000584905002
PDB chain4yq7 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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PDB4yq7 Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Resolution1.8 Å
Binding residue
(original residue number in PDB)		Y86 L87 S88 P89 S132 I133 Y136 L138 G140 P144
Binding residue
(residue number reindexed from 1)		Y89 L90 S91 P92 S135 I136 Y139 L141 G143 P147
Annotation score1
Binding affinityBindingDB: IC50=6310nM
Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154
Catalytic site (residue number reindexed from 1) P92 E119 R157
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4yq7, PDBe:4yq7, PDBj:4yq7
PDBsum4yq7
PubMed
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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