Structure of PDB 6qrd Chain A Binding Site BS01

Receptor Information
>6qrd Chain A (length=212) Species: 36809 (Mycobacteroides abscessus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMKIDVVTIFPEYLQPVRQSLPGKAIDAGLVDVAVHDLRRWTHDVHKSVD
DSPYGGGPGMVMKPTVWGDALDEICTSETLLVVPTPAGYPFTQETAWQWS
TEDHLVIACGRYEGIDQRVADDAATRMRVREVSIGDYVLNGGEAAALVII
EAVLRLVPGVLSLLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWRAEQS
RQRTIERRPDLL
Ligand information
Ligand IDJEH
InChIInChI=1S/C27H31N7/c1-19(2)33-13-11-32(12-14-33)17-20-3-5-21(6-4-20)18-34-10-9-22-7-8-23(15-25(22)34)26-24(16-28)27(29)31-30-26/h3-10,15,19H,11-14,17-18H2,1-2H3,(H3,29,30,31)
InChIKeyZLJXHHAUABPXJM-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)N1CCN(CC1)Cc2ccc(cc2)Cn3ccc4c3cc(cc4)c5c(c([nH]n5)N)C#N
CACTVS 3.385CC(C)N1CCN(CC1)Cc2ccc(Cn3ccc4ccc(cc34)c5n[nH]c(N)c5C#N)cc2
FormulaC27 H31 N7
Name5-azanyl-3-[1-[[4-[(4-propan-2-ylpiperazin-1-yl)methyl]phenyl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile
ChEMBLCHEMBL4567409
DrugBank
ZINC
PDB chain6qrd 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]
PDB6qrd Development of Inhibitors againstMycobacterium abscessustRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		P83 T84 P85 G109 R110 Y111 S132 I133 G134 Y136 V137 L138 N139 G140 G141 A144
Binding residue
(residue number reindexed from 1)		P84 T85 P86 G110 R111 Y112 S133 I134 G135 Y137 V138 L139 N140 G141 G142 A145
Annotation score1
Binding affinityMOAD: Kd=100nM
PDBbind-CN: -logKd/Ki=7.00,Kd=100nM
Enzymatic activity
Catalytic site (original residue number in PDB) P85 E112 R154
Catalytic site (residue number reindexed from 1) P86 E113 R155
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:6qrd, PDBe:6qrd, PDBj:6qrd
PDBsum6qrd
PubMed31282680
UniProtB1MDI3

[Back to BioLiP]