Structure of PDB 6qr4 Chain B Binding Site BS01

Receptor Information
>6qr4 Chain B (length=205) Species: 36809 (Mycobacteroides abscessus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMKIDVVTIFPEYLQPVGLVDVAVHDLRRWTHDVHKSVDDSPYGGGPGMV
MKPTVWGDALDEICTSETLLVVPTPAGYPFTQETAWQWSTEDHLVIACGR
YEGIDQRVADDAATRMRVREVSIGDYVLNGGEAAALVIIEAVLRLVPGVS
LLEGPSYTRPPSWRGMDVPPVLLSGDHAKIAAWRAEQSRQRTIERRPDLL
GFDSP
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 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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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 I133 G134 Y136 L138 N139 G140 G141
Binding residue
(residue number reindexed from 1)		P73 T74 P75 G99 R100 Y101 S122 I123 G124 Y126 L128 N129 G130 G131
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) 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:6qr4, PDBe:6qr4, PDBj:6qr4
PDBsum6qr4
PubMed31282680
UniProtB1MDI3

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