Structure of PDB 4mcb Chain A Binding Site BS01

Receptor Information
>4mcb Chain A (length=205) 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
AVARFIPGVLGLLDCPHYTRPEVLEGLTVPPVLMSHHEEIRKWRLKQSLQ
RTWLR
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
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
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)		L87 S88 P89 E116 S132 I133 Y136 L138 G140 G141 P144
Binding residue
(residue number reindexed from 1)		L87 S88 P89 E116 S132 I133 Y136 L138 G140 G141 P144
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
Catalytic site (residue number reindexed from 1) P89 E116 R154
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4mcb, PDBe:4mcb, PDBj:4mcb
PDBsum4mcb
PubMed23981144
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

[Back to BioLiP]