Structure of PDB 4mcb Chain B Binding Site BS01

Receptor Information
>4mcb Chain B (length=243) Species: 71421 (Haemophilus influenzae Rd KW20) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVD
DRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVT
ELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLID
AVARFIPGVLGKQASAEEDSFADGLLDCPHYTRPEVLEGLTVPPVLMSGH
HEEIRKWRLKQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAE
Ligand information
Ligand ID21W
InChIInChI=1S/C19H18N6O2S/c26-17(14-10-28-19-16(14)18(27)24-11-25-19)23-8-13-3-1-12(2-4-13)7-20-9-15-21-5-6-22-15/h1-6,10-11,20H,7-9H2,(H,21,22)(H,23,26)(H,24,25,27)
InChIKeyRLANZYKQCHLLJS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6c1cc(ccc1CNCc2[nH]ccn2)CNC(=O)c3csc4c3C(=O)NC=N4
ACDLabs 12.01O=C2NC=Nc1scc(c12)C(=O)NCc3ccc(cc3)CNCc4nccn4
CACTVS 3.385O=C(NCc1ccc(CNCc2[nH]ccn2)cc1)c3csc4N=CNC(=O)c34
FormulaC19 H18 N6 O2 S
NameN-(4-{[(1H-imidazol-2-ylmethyl)amino]methyl}benzyl)-4-oxo-3,4-dihydrothieno[2,3-d]pyrimidine-5-carboxamide
ChEMBLCHEMBL2432011
DrugBank
ZINCZINC000095920768
PDB chain4mcb Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4mcb Selective Inhibitors of Bacterial t-RNA-(N(1)G37) Methyltransferase (TrmD) That Demonstrate Novel Ordering of the Lid Domain.
Resolution1.94 Å
Binding residue
(original residue number in PDB)		D169 A172 D173
Binding residue
(residue number reindexed from 1)		D169 A172 D173
Annotation score1
Binding affinityMOAD: ic50=1.5uM
PDBbind-CN: -logKd/Ki=5.82,IC50=1.5uM
Enzymatic activity
Catalytic site (original residue number in PDB) P89 E116 R154 D169
Catalytic site (residue number reindexed from 1) P89 E116 R154 D169
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:4mcb, PDBe:4mcb, PDBj:4mcb
PDBsum4mcb
PubMed23981144
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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