Structure of PDB 6q8b Chain A Binding Site BS01

Receptor Information
>6q8b Chain A (length=834) 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
FLQVYTTRPDTLMGATYVAVAAEHPLATAAAADKPELQAFIAECKAGADM
ATMEKKGVPTGRYVVNPLNGDKLEVWIANYVLWGYGDGAVMAVPAHDERD
FEFAAKYNLPKKQVIAVGDNAFDANRWQEWYGDKENGVLVNSGDLDGLDF
QTAFDAVAAKLQSQGAGEPKTQYRLRDWGISRQRYWGCPIPIVHCEKCGN
VPVPADQLPVVLPENVVPDGMGSPLAKMPEFYETSCPCCGGAAKRETDTM
DTFIESSWYFFRYMSPKFSDGMVSAESAKYWGAVDQYIGGIEHAILHLLY
ARFFTKLMRDEGLVNVDEPFERLLTQGMVVCETYYWINPADVELTPVVIS
GTEKMSKSKNNGVDPQELINAYGADTARLFMMFAAPPEQSLEWSDSGVEG
AHRFLRRLWRTVYEYLKQGGAVKAFAGNQDGLSKELKDLRHKLHSTTAKV
SDDYGRRQQFNTAIAAVMELLNQYDKTDTGSEQGRAVAQEVLEAAVRLLW
PIVPHICETLWSELNGAKLWEAGWPTVDEAALVKSEIGKLRGKITVAADA
SKADLEAAALANEGAVKFMEGKIIVVPGRLVNIV
Ligand information
Ligand IDL3U
InChIInChI=1S/C16H26N4O9S/c1-8(2)6-9(17)14(24)18-30(26,27)28-7-10-12(22)13(23)15(29-10)20-5-4-11(21)19(3)16(20)25/h4-5,8-10,12-13,15,22-23H,6-7,17H2,1-3H3,(H,18,24)/t9-,10+,12+,13+,15+/m0/s1
InChIKeyIHQCOGYAMSEDBL-KHBBOIOASA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=CC(=O)N(C2=O)C)O)O)N
CACTVS 3.385CC(C)C[CH](N)C(=O)N[S](=O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)N2C=CC(=O)N(C)C2=O
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)N2C=CC(=O)N(C)C2=O
OpenEye OEToolkits 2.0.6CC(C)CC(C(=O)NS(=O)(=O)OCC1C(C(C(O1)N2C=CC(=O)N(C2=O)C)O)O)N
FormulaC16 H26 N4 O9 S
Name[(2~{R},3~{S},4~{R},5~{R})-5-[3-methyl-2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl ~{N}-[(2~{S})-2-azanyl-4-methyl-pentanoyl]sulfamate
ChEMBLCHEMBL4451258
DrugBank
ZINC
PDB chain6q8b Chain A Residue 901 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6q8b Comparative analysis of pyrimidine substituted aminoacyl-sulfamoyl nucleosides as potential inhibitors targeting class I aminoacyl-tRNA synthetases.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		M40 F41 P42 Y43 H49 G51 H52 N55 D80 G544 E546 H547 H551 Q580
Binding residue
(residue number reindexed from 1)		M40 F41 P42 Y43 H49 G51 H52 N55 D80 G540 E542 H543 H547 Q576
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.53,Ki=29.5nM
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 15 12:51:12 2024

A problem occurred in a Python script. Here is the sequence of function calls leading up to the error, in the order they occurred.

 /var/www/html/BioLiP/pdb.cgi in <module>()
   1435     title=pdb2title(pdbid)
   1436     if bs.startswith("BS"):
=> 1437         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)
   1438     else:
   1439         if lig3:
pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '6q8b', asym_id = 'A', bs = 'BS01', title = 'Comparative analysis of pyrimidine substituted a...rs targeting class I aminoacyl-tRNA synthetases. '
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6q8b', asym_id='A', bs='BS01', title='Comparative analysis of pyrimidine substituted a...rs targeting class I aminoacyl-tRNA synthetases. ')
   1295         display_ec(ec,csaOrig,csaRenu)
   1296     if go:
=> 1297         display_go(go,uniprot,pdbid,asym_id)
   1298     return pubmed,uniprot
   1299 
global display_go = <function display_go>, go = '0000166,0002161,0004812,0004823,0005524,0006418,0006429', uniprot = '', pdbid = '6q8b', asym_id = 'A'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000166,0002161,0004812,0004823,0005524,0006418,0006429', uniprot='', pdbid='6q8b', asym_id='A')
    480         '''.replace("$namespace_link",namespace_link
    481           ).replace("$namespace",namespace
=>  482           ).replace("$uniprot",u
    483         ))
    484         for l,(term,name) in enumerate(go2aspect[Aspect]):
u undefined

UnboundLocalError: local variable 'u' referenced before assignment
      args = ("local variable 'u' referenced before assignment",)
      with_traceback = <built-in method with_traceback of UnboundLocalError object>