Structure of PDB 5zhj Chain A Binding Site BS01

Receptor Information
>5zhj Chain A (length=206) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MRIDIVTIFPACLDPLRQSLPGKAIESGLVDLNVHDLRRWTHDVHHSVDD
APYGGGPGMVMKAPVWGEALDEICSSETLLIVPTPAGVLFTQATAQRWTT
ESHLVFACGRYEGIDQRVVQDAARRMRVEEVSIGDYVLPGGESAAVVMVE
AVLRLLAGVLGPSYTRPASWRGLDVPEVLLSGDHARIAAWRREVSLQRTR
ERRPDL
Ligand information
Ligand IDSAH
InChIInChI=1S/C14H20N6O5S/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKeyZJUKTBDSGOFHSH-WFMPWKQPSA-N
SMILES
SoftwareSMILES
CACTVS 3.341N[CH](CCSC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CSCCC(C(=O)O)N)O)O)N
CACTVS 3.341N[C@@H](CCSC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
ACDLabs 10.04O=C(O)C(N)CCSCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CSCC[C@@H](C(=O)O)N)O)O)N
FormulaC14 H20 N6 O5 S
NameS-ADENOSYL-L-HOMOCYSTEINE
ChEMBLCHEMBL418052
DrugBankDB01752
ZINCZINC000004228232
PDB chain5zhj 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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PDB5zhj Thienopyrimidinone Derivatives That Inhibit Bacterial tRNA (Guanine37-N1)-Methyltransferase (TrmD) by Restructuring the Active Site with a Tyrosine-Flipping Mechanism.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		P83 T84 P85 G109 E112 S132 I133 L138 G140 G141
Binding residue
(residue number reindexed from 1)		P83 T84 P85 G109 E112 S132 I133 L138 G140 G141
Annotation score5
Binding affinityMOAD: Kd=10.1uM
PDBbind-CN: -logKd/Ki=5.00,Kd=10.1uM
BindingDB: Kd=10100nM
Enzymatic activity
Catalytic site (original residue number in PDB) P85 E112 R154
Catalytic site (residue number reindexed from 1) P85 E112 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:5zhj, PDBe:5zhj, PDBj:5zhj
PDBsum5zhj
PubMed31442049
UniProtP9WFY7|TRMD_MYCTU tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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