Structure of PDB 7ap2 Chain A Binding Site BS01

Receptor Information
>7ap2 Chain A (length=843) Species: 485 (Neisseria gonorrhoeae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MQEHYQPAAIEPAAQKKWDDARISNVSEDASKPKYYCLSMFPYPSGKLHM
GHVRNYTIGDVLSRFKLLNGFNVMQPMGWDAFGMPAENAAMKNNVAPAAW
TYDNIEYMKTQLKSLGFAVDWEREVATCKPEYYRWEQWLFTKLFEKGIVY
RKNGTVNWDPVDQTVLANEQVIDGRGWRSGALIEKREIPMYYFKITDYAE
ELLNDLDKLEHWPEQVKTMQRNWIGKSRGMTVRFAVSDDSKQGLEGDYAK
FLQVYTTRPDTLMGATYVAVAAEHPLATAAAADKPELQAFIAECKAGSVA
EADMATMEKKGVPTGRYVVNPLNGDKLEVWIANYVLWGYGDGAVMAVPAH
DERDFEFAAKYNLPKKQVIAVGDNAFDANRWQEWYGDKENGVLVNSGDLD
GLDFQTAFDAVAAKLQSQGAGEPKTQYRLRDWGISRQRYWGCPIPIVHCE
KCGNVPVPADQLPVVLPENVVPDGMGSPLAKMPEFYETSCPCCGGAAKRE
TDTMDTFIESSWYFFRYMSPKFSDGMVSAESAKYWGAVDQYIGGIEHAIL
HLLYARFFTKLMRDEGLVNVDEPFERLLTQGMVVCETYYRENDKGGKDWI
NPADVELTSAVLKADGLPVVISGTEKMSKSKNNGVDPQELINAYGADTAR
LFMMFAAPPEQSLEWSDSGVEGAHRFLRRLWRTVYEYLKQGGAVKAFAGN
QDGLSKELKDLRHKLHSTTAKVSDDYGRRQQFNTAIAAVMELLNQYDKTD
TGSEQGRAVAQEVLEAAVRLLWPIVPHICETLWSELNGAKLWEAGWPTVD
EAALVKSEIRGKITVAADASKADLEAAALAKIIVVPGRLVNIV
Ligand information
Ligand IDRRW
InChIInChI=1S/C19H29N5O8S/c1-9(2)3-12(21)18(28)23-33(29,30)31-7-14-16(26)17(27)19(32-14)24-8-22-13-5-10(6-25)4-11(20)15(13)24/h4-5,8-9,12,14,16-17,19,25-27H,3,6-7,20-21H2,1-2H3,(H,23,28)/t12-,14+,16+,17+,19+/m0/s1
InChIKeyKLFPFKQOJXUPER-MVGUPFISSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2c(cc(c3)CO)N)O)O)N
CACTVS 3.385CC(C)C[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3cc(CO)cc(N)c23
OpenEye OEToolkits 2.0.7CC(C)CC(C(=O)NS(=O)(=O)OCC1C(C(C(O1)n2cnc3c2c(cc(c3)CO)N)O)O)N
CACTVS 3.385CC(C)C[C@H](N)C(=O)N[S](=O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3cc(CO)cc(N)c23
FormulaC19 H29 N5 O8 S
Name[(2~{R},3~{S},4~{R},5~{R})-5-[7-azanyl-5-(hydroxymethyl)benzimidazol-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate
ChEMBL
DrugBank
ZINC
PDB chain7ap2 Chain A Residue 1203 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7ap2 Synthesis and Biological Evaluation of 1,3-Dideazapurine-Like 7-Amino-5-Hydroxymethyl-Benzimidazole Ribonucleoside Analogues as Aminoacyl-tRNA Synthetase Inhibitors.
Resolution2.25 Å
Binding residue
(original residue number in PDB)		M40 F41 P42 Y43 H49 G51 H52 D80 G543 G544 E546 H547 H551 Q580 M582 V583
Binding residue
(residue number reindexed from 1)		M40 F41 P42 Y43 H49 G51 H52 D80 G543 G544 E546 H547 H551 Q580 M582 V583
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) F41 D80 F507 H547 F557 K634 K637
Catalytic site (residue number reindexed from 1) F41 D80 F507 H547 F557 K626 K629
Enzyme Commision number 6.1.1.4: leucine--tRNA ligase.
Gene Ontology
Molecular Function
GO:0000166 nucleotide binding
GO:0002161 aminoacyl-tRNA editing activity
GO:0004812 aminoacyl-tRNA ligase activity
GO:0004823 leucine-tRNA ligase activity
GO:0005524 ATP binding
Biological Process
GO:0006412 translation
GO:0006418 tRNA aminoacylation for protein translation
GO:0006429 leucyl-tRNA aminoacylation
GO:0106074 aminoacyl-tRNA metabolism involved in translational fidelity
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:7ap2, PDBe:7ap2, PDBj:7ap2
PDBsum7ap2
PubMed33081246
UniProtQ5FAJ3|SYL_NEIG1 Leucine--tRNA ligase (Gene Name=leuS)

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