Structure of PDB 6qr0 Chain A Binding Site BS01

Receptor Information
>6qr0 Chain A (length=215) Species: 36809 (Mycobacteroides abscessus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMKIDVVTIFPEYLQPVRQSLPGKAIDAGLVDVAVHDLRRWTHDVHKSVD
DSPYGGGPGMVMKPTVWGDALDEICTSETLLVVPTPAGYPFTQETAWQWS
TEDHLVIACGRYEGIDQRVADDAATRMRVREVSIGDYVLNGGEAAALVII
EAVLRLVPGVLGNASLLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWRA
EQSRQRTIERRPDLL
Ligand information
Ligand IDJFB
InChIInChI=1S/C18H14N6/c19-10-15-17(22-23-18(15)20)14-2-1-13-5-8-24(16(13)9-14)11-12-3-6-21-7-4-12/h1-9H,11H2,(H3,20,22,23)
InChIKeyMOYIETQNOXXROV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1[nH]nc(c2ccc3ccn(Cc4ccncc4)c3c2)c1C#N
OpenEye OEToolkits 2.0.7c1cc(cc2c1ccn2Cc3ccncc3)c4c(c([nH]n4)N)C#N
FormulaC18 H14 N6
Name5-azanyl-3-[1-(pyridin-4-ylmethyl)indol-6-yl]-1~{H}-pyrazole-4-carbonitrile
ChEMBLCHEMBL4576907
DrugBank
ZINC
PDB chain6qr0 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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PDB6qr0 Development of Inhibitors against Mycobacterium abscessus tRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.
Resolution1.59 Å
Binding residue
(original residue number in PDB)		P83 T84 P85 G109 R110 Y111 E112 S132 G134 Y136 V137 L138 N139 G140 G141
Binding residue
(residue number reindexed from 1)		P84 T85 P86 G110 R111 Y112 E113 S133 G135 Y137 V138 L139 N140 G141 G142
Annotation score1
Binding affinityMOAD: Kd=0.12uM
PDBbind-CN: -logKd/Ki=6.92,Kd=0.12uM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:6qr0, PDBe:6qr0, PDBj:6qr0
PDBsum6qr0
PubMed31282680
UniProtB1MDI3

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