Structure of PDB 4yqg Chain A Binding Site BS01

Receptor Information
>4yqg 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]
GSHMWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHK
TVDDRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQG
GVTELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMT
LIDAVARFIPGVLGDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWR
LKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHN
Ligand information
Ligand ID4GY
InChIInChI=1S/C10H16N4O2/c11-9-8(13-16-14-9)10(15)12-6-7-4-2-1-3-5-7/h7H,1-6H2,(H2,11,14)(H,12,15)
InChIKeyLMUMGZXENBDFGR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C1CCC(CC1)CNC(=O)c2c(non2)N
ACDLabs 12.01
CACTVS 3.385		Nc1nonc1C(=O)NCC2CCCCC2
FormulaC10 H16 N4 O2
Name4-amino-N-(cyclohexylmethyl)-1,2,5-oxadiazole-3-carboxamide
ChEMBL
DrugBank
ZINC
PDB chain4yqg Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB4yqg Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Resolution1.858 Å
Binding residue
(original residue number in PDB)		L87 S88 P89 S132 I133 L138 G140 P144
Binding residue
(residue number reindexed from 1)		L90 S91 P92 S135 I136 L141 G143 P147
Annotation score1
Binding affinityBindingDB: IC50=1995nM
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:4yqg, PDBe:4yqg, PDBj:4yqg
PDBsum4yqg
PubMed
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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