Structure of PDB 4qre Chain A Binding Site BS01

Receptor Information

>4qre Chain A (length=519) Species: 1280 (Staphylococcus aureus)

AKETFYITTPIYYPSGNLHIGHAYSTVAGDVIARYKRMQGYDVRYLTGTD
EHGQKIQEKAQKAGKTEIEYLDEMIAGIKQLWAKLEISNDDFIRTTEERH
KHVVEQVFERLLKQGDIYLGEYEGWYSVPDETYYTESQLVDPQYENGKII
GGKSPDSGHEVELVKEESYFFNISKYTDRLLEFYDQNPDFIQPPSRKNEM
INNFIKPGLADLAVSRTSFNWGVHVPSNPKHVVYVWIDALVNYISALGYL
SDDESLFNKYWPADIHLMAKEIVRFHSIIWPILLMALDLPLPKKVFAHGW
ILMKDGKMSKSKGNVVDPNILIDRYGLDATRYYLMRELPFGSDGVFTPEA
FVERTNFDLANDLGNLVNRTISMVNKYFDGELPAYQGPLHELDEEMEAMA
LETVKSYTESMESLQFSVALSTVWKFISRTNKYIDETTPWVLAKDDSQKD
MLGNVMAHLVENIRYAAVLLRPFLTHAPKEIFEQLNINNPQFMEFSSLEQ
YGVLTESIMVTGQPKPIFP

Ligand information

• Ligand ID: 3BG
• InChI: InChI=1S/C27H31N7O4/c1-17-13-22(36-3)23(37-4)14-21(17)38-26-15-24(28-16-25-29-19-7-5-6-8-20(19)30-25)31-27(32-26)34-11-9-33(10-12-34)18(2)35/h5-8,13-15H,9-12,16H2,1-4H3,(H,29,30)(H,28,31,32)
• InChIKey: QDJWEGQUTGIBNS-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: COc1cc(C)c(Oc2cc(NCc3[nH]c4ccccc4n3)nc(n2)N5CCN(CC5)C(C)=O)cc1OC
  ACDLabs 12.01: O=C(N5CCN(c4nc(NCc2nc1ccccc1n2)cc(Oc3cc(OC)c(OC)cc3C)n4)CC5)C
  OpenEye OEToolkits 1.7.6: Cc1cc(c(cc1Oc2cc(nc(n2)N3CCN(CC3)C(=O)C)NCc4[nH]c5ccccc5n4)OC)OC
• Formula: C27 H31 N7 O4
• Name: 1-(4-{4-[(1H-benzimidazol-2-ylmethyl)amino]-6-(4,5-dimethoxy-2-methylphenoxy)pyrimidin-2-yl}piperazin-1-yl)ethanone
• ZINC: ZINC000263620926
• PDB chain: 4qre Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4qre Discovery and SAR of a Novel Series of Pyrimidine Antibacterials Targeting Methionyl-tRNA Synthetase
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): P11 I12 Y14 D51 H53 T133 Y134 F220 V234 Y235 V236 D239 A240 Y244 I273 F276
• Binding residue (residue number reindexed from 1): P10 I11 Y13 D50 H52 T132 Y133 F219 V233 Y234 V235 D238 A239 Y243 I272 F275
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Feb 17 04:13:46 2025

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 = '4qre', asym_id = 'A', bs = 'BS01', title = 'Discovery and SAR of a Novel Series of Pyrimidine Antibacterials Targeting Methionyl-tRNA Synthetase'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4qre', asym_id='A', bs='BS01', title='Discovery and SAR of a Novel Series of Pyrimidine Antibacterials Targeting Methionyl-tRNA Synthetase')

   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 = '0000166,0004812,0004825,0005524,0006418,0006431', uniprot = '', pdbid = '4qre', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000166,0004812,0004825,0005524,0006418,0006431', uniprot='', pdbid='4qre', 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>