Structure of PDB 4mcd Chain A Binding Site BS01

Receptor Information
>4mcd 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]
MWIGVISLFPEMFKAITEFGVTGRAVKHNLLKVECWNPRDFTFDKHKTVD
DRPYGGGPGMLMMVQPLRDAIHTAKAAAGEGAKVIYLSPQGRKLDQGGVT
ELAQNQKLILVCGRYEGIDERLIQTEIDEEWSIGDYVLTGGELPAMTLID
AVARFIPGVLSFADGLLDCPHYTRPEVLEGLTVPPVLMSGHHEEIRKWRL
KQSLQRTWLRRPELLEGLALTDEQRKLLKEAQAEHNS
Ligand information
Ligand ID22L
InChIInChI=1S/C12H8N2OS/c15-11-10-9(8-4-2-1-3-5-8)6-16-12(10)14-7-13-11/h1-7H,(H,13,14,15)
InChIKeyOLGMRBGIXZANNV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C2NC=Nc1scc(c12)c3ccccc3
OpenEye OEToolkits 1.7.6c1ccc(cc1)c2csc3c2C(=O)NC=N3
CACTVS 3.385O=C1NC=Nc2scc(c3ccccc3)c12
FormulaC12 H8 N2 O S
Name5-phenylthieno[2,3-d]pyrimidin-4(3H)-one
ChEMBLCHEMBL1369722
DrugBank
ZINCZINC000008578704
PDB chain4mcd 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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PDB4mcd Selective Inhibitors of Bacterial t-RNA-(N(1)G37) Methyltransferase (TrmD) That Demonstrate Novel Ordering of the Lid Domain.
Resolution1.55 Å
Binding residue
(original residue number in PDB)		L87 S88 P89 S132 I133 Y136 L138 G140 P144
Binding residue
(residue number reindexed from 1)		L87 S88 P89 S132 I133 Y136 L138 G140 P144
Annotation score1
Binding affinityMOAD: ic50=4.7uM
PDBbind-CN: -logKd/Ki=5.33,IC50=4.7uM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:4mcd, PDBe:4mcd, PDBj:4mcd
PDBsum4mcd
PubMed23981144
UniProtP43912|TRMD_HAEIN tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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