Structure of PDB 6qra Chain B Binding Site BS01

Receptor Information
>6qra Chain B (length=206) Species: 36809 (Mycobacteroides abscessus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMKIDVVTIFPEYLQPVGLVDVAVHDLRRWTHDVHKSVDDSPYGGGPGMV
MKPTVWGDALDEICTSETLLVVPTPAGYPFTQETAWQWSTEDHLVIACGR
YEGIDQRVADDAATRMRVREVSIGDYVLNGGEAAALVIIEAVLRLVPGVA
SLLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWRAEQSRQRTIERRPDL
LGFDSP
Ligand information
Ligand IDJDK
InChIInChI=1S/C24H27N5/c25-24-15-22(26-27-24)21-9-8-20-10-13-29(23(20)14-21)17-19-6-4-18(5-7-19)16-28-11-2-1-3-12-28/h4-10,13-15H,1-3,11-12,16-17H2,(H3,25,26,27)
InChIKeyVDYQWEHGAZCAGH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Nc1[nH]nc(c1)c2ccc3ccn(Cc4ccc(CN5CCCCC5)cc4)c3c2
OpenEye OEToolkits 2.0.7c1cc(ccc1Cn2ccc3c2cc(cc3)c4cc([nH]n4)N)CN5CCCCC5
FormulaC24 H27 N5
Name3-[1-[[4-(piperidin-1-ylmethyl)phenyl]methyl]indol-6-yl]-1~{H}-pyrazol-5-amine
ChEMBLCHEMBL4459768
DrugBank
ZINC
PDB chain6qra Chain B Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6qra Development of Inhibitors againstMycobacterium abscessustRNA (m1G37) Methyltransferase (TrmD) Using Fragment-Based Approaches.
Resolution1.71 Å
Binding residue
(original residue number in PDB)		P83 T84 P85 G109 R110 Y111 E112 S132 I133 G134 Y136 L138 N139 G140 G141
Binding residue
(residue number reindexed from 1)		P73 T74 P75 G99 R100 Y101 E102 S122 I123 G124 Y126 L128 N129 G130 G131
Annotation score1
Binding affinityMOAD: Kd=710nM
PDBbind-CN: -logKd/Ki=6.15,Kd=710nM
Enzymatic activity
Catalytic site (original residue number in PDB) P85 E112 R154
Catalytic site (residue number reindexed from 1) P75 E102 R144
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:6qra, PDBe:6qra, PDBj:6qra
PDBsum6qra
PubMed31282680
UniProtB1MDI3

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