Structure of PDB 7qi8 Chain A Binding Site BS02

Receptor Information
>7qi8 Chain A (length=462) Species: 83332 (Mycobacterium tuberculosis H37Rv) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EQFRIRRDKRARLLAQGRDPYPVAVPRTHTLAEVRAAHPDLPIDTATEDI
VGVAGRVIFARNSGKLCFATLQDGDGTQLQVMISLDKVGQAALDAWKADV
DLGDIVYVHGAVISSRELSVLADCWRIAAKSLRPLPVMSEESRVRQRYVD
LIVRPEARAVARLRIAVVRAIRTALQRRGFLEVETPVLQTLAGGAAARPF
ATHSNALDIDLYLRIAPELFLKRCIVGGFDKVFELNRVFRNEGADSTHSP
EFSMLETYQTYGTYDDSAVVTRELIQEVADEAIGTRQLPLPDGSVYDIDG
EWATIQMYPSLSVALGEEITPQTTVDRLRGIADSLGFGHGKLIEELWERT
VGKSLSAPTFVKDFPVQTTPLTRQHRSIPGVTEKWDLYLRGIELATGYSE
LSDPVVQRERFADQARAAVLDEDFLAALEYGMPPCTGTGMGIDRLLMSLT
GLSIRETVLFPI
Ligand information
Ligand IDDD0
InChIInChI=1S/C14H18F2N4O3/c1-23-11-9-7(18-13(17)19-11)6-20(12(9)22)10-8(21)4-2-3-5-14(10,15)16/h8,10,21H,2-6H2,1H3,(H2,17,18,19)/t8-,10-/m0/s1
InChIKeyVWSRMVWRUFUXMB-WPRPVWTQSA-N
SMILES
SoftwareSMILES
CACTVS 3.385COc1nc(N)nc2CN([CH]3[CH](O)CCCCC3(F)F)C(=O)c12
OpenEye OEToolkits 2.0.7COc1c2c(nc(n1)N)CN(C2=O)[C@H]3[C@H](CCCCC3(F)F)O
OpenEye OEToolkits 2.0.7COc1c2c(nc(n1)N)CN(C2=O)C3C(CCCCC3(F)F)O
CACTVS 3.385COc1nc(N)nc2CN([C@H]3[C@@H](O)CCCCC3(F)F)C(=O)c12
FormulaC14 H18 F2 N4 O3
Name2-azanyl-6-[(1~{S},7~{S})-2,2-bis(fluoranyl)-7-oxidanyl-cycloheptyl]-4-methoxy-7~{H}-pyrrolo[3,4-d]pyrimidin-5-one
ChEMBL
DrugBank
ZINC
PDB chain7qi8 Chain A Residue 602 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7qi8 Lysyl-tRNA synthetase, a target for urgently needed M. tuberculosis drugs.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		R257 E259 T264 H265 S266 F269 L423 A424 T425 M477 G478 R481
Binding residue
(residue number reindexed from 1)		R240 E242 T247 H248 S249 F252 L394 A395 T396 M440 G441 R444
Annotation score1
Enzymatic activity
Enzyme Commision number 6.1.1.6: lysine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000049 tRNA binding
GO:0000166 nucleotide binding
GO:0000287 magnesium ion binding
GO:0003676 nucleic acid binding
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004824 lysine-tRNA ligase activity
GO:0005524 ATP binding
GO:0046872 metal ion binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006430 lysyl-tRNA aminoacylation
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:7qi8, PDBe:7qi8, PDBj:7qi8
PDBsum7qi8
PubMed36220877
UniProtP9WFU9|SYK1_MYCTU Lysine--tRNA ligase 1 (Gene Name=lysS1)

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