Structure of PDB 7db8 Chain A Binding Site BS03

Receptor Information
>7db8 Chain A (length=267) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DERLATLRAERDAAVLVAEGIDVTLPSTRVPAGARHPIIMLAEHVADTFI
AMGWELAEGPEVETEQFNFDALNFPADHPARGEQDTFYIAPEDSRQLLRT
HTSPVQIRTLLARELPVYIISIGRTFRTDELDATHTPIFHQVEGLAVDRG
LSMAHLRGTLDAFARAEFGPSARTRIRPHFFPFTEPSAEVDVWFANKIGG
AAWVEWGGCGMVHPNVLRATGIDPDLYSGFAFGMGLERTLQFRNGIPDMR
DMVEGDVRFSLPFGVGA
Ligand information
Ligand IDH2R
InChIInChI=1S/C24H23F3N4O2/c25-24(26,27)19-6-7-22(29-15-19)33-21-5-1-3-18(14-21)13-17-8-11-31(12-9-17)23(32)30-20-4-2-10-28-16-20/h1-7,10,14-17H,8-9,11-13H2,(H,30,32)
InChIKeyNBOJHRYUGLRASX-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1cc(cc(c1)Oc2ccc(cn2)C(F)(F)F)CC3CCN(CC3)C(=O)Nc4cccnc4
CACTVS 3.385FC(F)(F)c1ccc(Oc2cccc(CC3CCN(CC3)C(=O)Nc4cccnc4)c2)nc1
FormulaC24 H23 F3 N4 O2
NameN-pyridin-3-yl-4-[[3-[5-(trifluoromethyl)pyridin-2-yl]oxyphenyl]methyl]piperidine-1-carboxamide
ChEMBLCHEMBL1651524
DrugBank
ZINCZINC000043205344
PDB chain7db8 Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7db8 Re-discovery of PF-3845 as a new chemical scaffold inhibiting phenylalanyl-tRNA synthetase in Mycobacterium tuberculosis .
Resolution2.3 Å
Binding residue
(original residue number in PDB)		L146 S177 R201 F213 Q215 E217 L219 F255 F257 G282 C283 A305 F306 G307 G309 R312
Binding residue
(residue number reindexed from 1)		L72 S103 R127 F139 Q141 E143 L145 F181 F183 G208 C209 A231 F232 G233 G235 R238
Annotation score1
Enzymatic activity
Enzyme Commision number 6.1.1.20: phenylalanine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004826 phenylalanine-tRNA ligase activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006432 phenylalanyl-tRNA aminoacylation
GO:0043039 tRNA aminoacylation
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7db8, PDBe:7db8, PDBj:7db8
PDBsum7db8
PubMed33397709
UniProtP9WFU3|SYFA_MYCTU Phenylalanine--tRNA ligase alpha subunit (Gene Name=pheS)

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