Structure of PDB 6afk Chain B Binding Site BS02

Receptor Information
>6afk Chain B (length=245) Species: 208963 (Pseudomonas aeruginosa UCBPP-PA14) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SMLWVGVVSIFPEMFRAISDYGITSRAVKQGLLTLTCWNPRVYTEDRHQT
VDDRPFGGGPGMVMKIKPLEGALADARQAAGGRKAKVIYLSPQGRQLTQA
GVRELAEEEALILIAGRYEGIDERFIEEHVDEEWSIGDYVLSGGELPAMV
LVDAVTRLLPGALDSAEEDSFTDGLLDCPHYTRPEVYADKRVPEVLLSGN
HEHIRRWRLQQALGRTWERRADLLDSRSLSGEEQKLLAEYIRQRD
Ligand information
Ligand ID9WO
InChIInChI=1S/C22H22N6O/c29-22(20-12-16-4-1-2-6-18(16)25-20)24-17-5-3-11-28(14-17)21-13-19(26-27-21)15-7-9-23-10-8-15/h1-2,4,6-10,12-13,17,25H,3,5,11,14H2,(H,24,29)(H,26,27)/t17-/m0/s1
InChIKeyZFKKLBZXLNWYEO-KRWDZBQOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385O=C(N[CH]1CCCN(C1)c2[nH]nc(c2)c3ccncc3)c4[nH]c5ccccc5c4
CACTVS 3.385O=C(N[C@H]1CCCN(C1)c2[nH]nc(c2)c3ccncc3)c4[nH]c5ccccc5c4
OpenEye OEToolkits 2.0.6c1ccc2c(c1)cc([nH]2)C(=O)NC3CCCN(C3)c4cc(n[nH]4)c5ccncc5
ACDLabs 12.01c2c1ccccc1nc2C(NC3CCCN(C3)c4cc(nn4)c5ccncc5)=O
OpenEye OEToolkits 2.0.6c1ccc2c(c1)cc([nH]2)C(=O)N[C@H]3CCCN(C3)c4cc(n[nH]4)c5ccncc5
FormulaC22 H22 N6 O
NameN-{(3S)-1-[3-(pyridin-4-yl)-1H-pyrazol-5-yl]piperidin-3-yl}-1H-indole-2-carboxamide
ChEMBL
DrugBank
ZINCZINC000096124852
PDB chain6afk 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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PDB6afk Targeting the Bacterial Epitranscriptome for Antibiotic Development: Discovery of Novel tRNA-(N1G37) Methyltransferase (TrmD) Inhibitors.
Resolution2.75 Å
Binding residue
(original residue number in PDB)		S93 Y120 E121 G122 S137 I138 Y141 L143 S144 G145 P149
Binding residue
(residue number reindexed from 1)		S91 Y118 E119 G120 S135 I136 Y139 L141 S142 G143 P147
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) P94 E121 R159 D174
Catalytic site (residue number reindexed from 1) P92 E119 R157 D169
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:6afk, PDBe:6afk, PDBj:6afk
PDBsum6afk
PubMed30682246
UniProtQ02RL6|TRMD_PSEAB tRNA (guanine-N(1)-)-methyltransferase (Gene Name=trmD)

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