Structure of PDB 4yqo Chain A Binding Site BS01

Receptor Information
>4yqo 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]
GLVPRGSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFT
FDKHKTVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGR
KLDQGGVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGE
LPAMTLIDAVARFIPGVLDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEI
RKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Ligand information
Ligand ID4H1
InChIInChI=1S/C14H22N4O/c15-7-10-2-1-3-11(6-10)8-17-13-5-4-12(9-18-13)14(16)19/h4-5,9-11H,1-3,6-8,15H2,(H2,16,19)(H,17,18)/t10-,11+/m0/s1
InChIKeyUUTSJGSKPMLQOF-WDEREUQCSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01c1c(cnc(c1)NCC2CCCC(C2)CN)C(N)=O
OpenEye OEToolkits 1.9.2c1cc(ncc1C(=O)N)NC[C@@H]2CCC[C@@H](C2)CN
OpenEye OEToolkits 1.9.2c1cc(ncc1C(=O)N)NCC2CCCC(C2)CN
CACTVS 3.385NC[C@H]1CCC[C@@H](CNc2ccc(cn2)C(N)=O)C1
CACTVS 3.385NC[CH]1CCC[CH](CNc2ccc(cn2)C(N)=O)C1
FormulaC14 H22 N4 O
Name6-({[(1R,3S)-3-(aminomethyl)cyclohexyl]methyl}amino)pyridine-3-carboxamide
ChEMBL
DrugBank
ZINCZINC000311876079
PDB chain4yqo 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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PDB4yqo Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Resolution1.68 Å
Binding residue
(original residue number in PDB)		L87 S88 P89 E116 S132 I133 Y136 L138 G140 P144
Binding residue
(residue number reindexed from 1)		L95 S96 P97 E124 S140 I141 Y144 L146 G148 P152
Annotation score1
Binding affinityBindingDB: IC50=501nM
Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154
Catalytic site (residue number reindexed from 1) P97 E124 R162
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:4yqo, PDBe:4yqo, PDBj:4yqo
PDBsum4yqo
PubMed
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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