Structure of PDB 4ypz Chain A Binding Site BS01

Receptor Information
>4ypz Chain A (length=236) 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
IDAVARFIPGVLDGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRLK
QSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Ligand information
Ligand ID4FL
InChIInChI=1S/C8H7N3/c1-3-9-4-2-7(1)8-10-5-6-11-8/h1-6H,(H,10,11)
InChIKeyQWZSAEUNIBEKIZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385[nH]1ccnc1c2ccncc2
OpenEye OEToolkits 1.9.2c1cnccc1c2[nH]ccn2
ACDLabs 12.01c1c(ccnc1)c2nccn2
FormulaC8 H7 N3
Name4-(1H-imidazol-2-yl)pyridine
ChEMBLCHEMBL3274310
DrugBank
ZINCZINC000013283576
PDB chain4ypz 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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PDB4ypz Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds
Resolution1.84 Å
Binding residue
(original residue number in PDB)		L87 S88 P89 I133 L138 G140 G141 P144
Binding residue
(residue number reindexed from 1)		L89 S90 P91 I135 L140 G142 G143 P146
Annotation score1
Binding affinityBindingDB: IC50=316228nM
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:4ypz, PDBe:4ypz, PDBj:4ypz
PDBsum4ypz
PubMed
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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