Structure of PDB 4yq9 Chain A Binding Site BS01

Receptor Information
>4yq9 Chain A (length=245) 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
PAMTLIDAVARFIPGVLGSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHH
EEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Ligand information
Ligand ID4GO
InChIInChI=1S/C11H15N3O/c12-11(15)8-5-6-10(13-7-8)14-9-3-1-2-4-9/h5-7,9H,1-4H2,(H2,12,15)(H,13,14)
InChIKeyHTKJVDABQHUEPR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1c(cnc(c1)NC2CCCC2)C(=O)N
OpenEye OEToolkits 1.9.2c1cc(ncc1C(=O)N)NC2CCCC2
CACTVS 3.385NC(=O)c1ccc(NC2CCCC2)nc1
FormulaC11 H15 N3 O
Name6-(cyclopentylamino)pyridine-3-carboxamide
ChEMBLCHEMBL5276604
DrugBank
ZINC
PDB chain4yq9 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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PDB4yq9 Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Resolution1.64 Å
Binding residue
(original residue number in PDB)		L87 S88 P89 G113 S132 I133 Y136 L138 P144
Binding residue
(residue number reindexed from 1)		L94 S95 P96 G120 S139 I140 Y143 L145 P151
Annotation score1
Binding affinityBindingDB: IC50=200nM
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:4yq9, PDBe:4yq9, PDBj:4yq9
PDBsum4yq9
PubMed
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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