Structure of PDB 6qr4 Chain A Binding Site BS01

Receptor Information
>6qr4 Chain A (length=216) Species: 36809 (Mycobacteroides abscessus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSMKIDVVTIFPEYLQPVRQSLPGKAIDAGLVDVAVHDLRRWTHDVHKSV
DDSPYGGGPGMVMKPTVWGDALDEICTSETLLVVPTPAGYPFTQETAWQW
STEDHLVIACGRYEGIDQRVADDAATRMRVREVSIGDYVLNGGEAAALVI
IEAVLRLVPGVLGNASLLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWR
AEQSRQRTIERRPDLL
Ligand information
Ligand IDJD8
InChIInChI=1S/C19H22N6/c1-24-8-3-2-4-15(24)12-25-9-7-13-5-6-14(10-17(13)25)18-16(11-20)19(21)23-22-18/h5-7,9-10,15H,2-4,8,12H2,1H3,(H3,21,22,23)/t15-/m1/s1
InChIKeySXMWJVDDIHQQEA-OAHLLOKOSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CN1CCCCC1Cn2ccc3c2cc(cc3)c4c(c([nH]n4)N)C#N
CACTVS 3.385CN1CCCC[CH]1Cn2ccc3ccc(cc23)c4n[nH]c(N)c4C#N
CACTVS 3.385CN1CCCC[C@@H]1Cn2ccc3ccc(cc23)c4n[nH]c(N)c4C#N
OpenEye OEToolkits 2.0.7CN1CCCC[C@@H]1Cn2ccc3c2cc(cc3)c4c(c([nH]n4)N)C#N
FormulaC19 H22 N6
Name5-azanyl-3-[1-[[(2~{R})-1-methylpiperidin-2-yl]methyl]indol-6-yl]-1~{H}-pyrazole-4-carbonitrile
ChEMBL
DrugBank
ZINC
PDB chain6qr4 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

[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]
PDB6qr4 Development of Inhibitors against Mycobacterium abscessus tRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.
Resolution1.52 Å
Binding residue
(original residue number in PDB)		P83 T84 P85 G109 R110 Y111 S132 G134 Y136 V137 L138 N139 G140 G141 A144
Binding residue
(residue number reindexed from 1)		P85 T86 P87 G111 R112 Y113 S134 G136 Y138 V139 L140 N141 G142 G143 A146
Annotation score1
Binding affinityMOAD: Kd=0.59uM
PDBbind-CN: -logKd/Ki=6.23,Kd=0.59uM
Enzymatic activity
Catalytic site (original residue number in PDB) P85 E112 R154
Catalytic site (residue number reindexed from 1) P87 E114 R156
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:6qr4, PDBe:6qr4, PDBj:6qr4
PDBsum6qr4
PubMed31282680
UniProtB1MDI3

[Back to BioLiP]