Structure of PDB 4yq5 Chain A Binding Site BS01

Receptor Information
>4yq5 Chain A (length=244) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPRGSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTF
DKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRK
LDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGEL
PAMTLIDAVARFIPGVLSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHE
EIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Ligand information
Ligand ID4G0
InChIInChI=1S/C15H18N4O/c1-19(2)13-5-3-4-11(8-13)9-17-14-7-6-12(10-18-14)15(16)20/h3-8,10H,9H2,1-2H3,(H2,16,20)(H,17,18)
InChIKeyRDIFHHLWNIKHIH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1cc(cc(c1)N(C)C)CNc2ccc(cn2)C(=O)N
CACTVS 3.385CN(C)c1cccc(CNc2ccc(cn2)C(N)=O)c1
OpenEye OEToolkits 1.9.2CN(C)c1cccc(c1)CNc2ccc(cn2)C(=O)N
FormulaC15 H18 N4 O
Name6-{[3-(dimethylamino)benzyl]amino}pyridine-3-carboxamide
ChEMBL
DrugBank
ZINCZINC000584905024
PDB chain4yq5 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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PDB4yq5 Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Resolution1.76 Å
Binding residue
(original residue number in PDB)		Y86 L87 S88 P89 E116 S132 I133 Y136 L138 G140 P144
Binding residue
(residue number reindexed from 1)		Y93 L94 S95 P96 E123 S139 I140 Y143 L145 G147 P151
Annotation score1
Binding affinityBindingDB: IC50=3981nM
Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154
Catalytic site (residue number reindexed from 1) P96 E123 R161
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:4yq5, PDBe:4yq5, PDBj:4yq5
PDBsum4yq5
PubMed
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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