Structure of PDB 4yq8 Chain A Binding Site BS01

Receptor Information
>4yq8 Chain A (length=240) 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
IDAVARFIPGVLGSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRK
WRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Ligand information
Ligand ID4FV
InChIInChI=1S/C8H12N4O3/c9-7-6(11-15-12-7)8(14)10-4-1-2-5(13)3-4/h4-5,13H,1-3H2,(H2,9,12)(H,10,14)/t4-,5+/m1/s1
InChIKeyUDKGUOUTPCVPOO-UHNVWZDZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2C1CC(CC1NC(=O)c2c(non2)N)O
OpenEye OEToolkits 1.9.2C1C[C@@H](C[C@@H]1NC(=O)c2c(non2)N)O
CACTVS 3.385Nc1nonc1C(=O)N[CH]2CC[CH](O)C2
CACTVS 3.385Nc1nonc1C(=O)N[C@@H]2CC[C@H](O)C2
ACDLabs 12.01c1(c(non1)N)C(=O)NC2CCC(C2)O
FormulaC8 H12 N4 O3
Name4-amino-N-[(1R,3S)-3-hydroxycyclopentyl]-1,2,5-oxadiazole-3-carboxamide
ChEMBL
DrugBank
ZINCZINC000584905039
PDB chain4yq8 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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PDB4yq8 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 R114 Y115 I133 Y136 L138 G140 P144
Binding residue
(residue number reindexed from 1)		L89 S90 P91 R116 Y117 I135 Y138 L140 G142 P146
Annotation score1
Binding affinityBindingDB: IC50=7943nM
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:4yq8, PDBe:4yq8, PDBj:4yq8
PDBsum4yq8
PubMed
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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