Structure of PDB 4yqj Chain A Binding Site BS01

Receptor Information
>4yqj Chain A (length=237) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKT
VDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGG
VTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTL
IDAVARFIPGVLGDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRL
KQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Ligand information
Ligand ID4GT
InChIInChI=1S/C10H15N5O/c11-8-7(9(12)16)5-13-10(15-8)14-6-3-1-2-4-6/h5-6H,1-4H2,(H2,12,16)(H3,11,13,14,15)
InChIKeyNNNGDGCCKKOXPR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385NC(=O)c1cnc(NC2CCCC2)nc1N
OpenEye OEToolkits 1.9.2c1c(c(nc(n1)NC2CCCC2)N)C(=O)N
ACDLabs 12.01c1c(C(N)=O)c(nc(n1)NC2CCCC2)N
FormulaC10 H15 N5 O
Name4-amino-2-(cyclopentylamino)pyrimidine-5-carboxamide
ChEMBLCHEMBL2030357
DrugBank
ZINCZINC000084668350
PDB chain4yqj 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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PDB4yqj Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Resolution1.94 Å
Binding residue
(original residue number in PDB)		L87 S88 P89 G117 S132 I133 Y136 L138 T139 G140 P144
Binding residue
(residue number reindexed from 1)		L89 S90 P91 G119 S134 I135 Y138 L140 T141 G142 P146
Annotation score1
Binding affinityBindingDB: IC50=631nM
Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154
Catalytic site (residue number reindexed from 1) P91 E118 R156
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:4yqj, PDBe:4yqj, PDBj:4yqj
PDBsum4yqj
PubMed
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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