Structure of PDB 4urn Chain A Binding Site BS01

Receptor Information

>4urn Chain A (length=188) Species: 1280 (Staphylococcus aureus)

LEGLEAVRKRPGMYIGSTDKRGLHHLVYEIVDNSVDEVLNGYGNEIDVTI
NKDGSISIEDNGRGMPTGIHKSGKPTVEVIFTVLVGASVVNALSEWLEVE
IHRDGNIYHQSFKNGGSPSSGLVKKGKTKKTGTKVTFKPDDTIFKASTSF
NFDVLSERLQESAFLLKNLKITLNDLRSGKERQEHYHY

Ligand information

• Ligand ID: NOV
• InChI: InChI=1S/C31H36N2O11/c1-14(2)7-8-16-13-17(9-11-19(16)34)27(37)33-21-22(35)18-10-12-20(15(3)24(18)42-28(21)38)41-29-23(36)25(43-30(32)39)26(40-6)31(4,5)44-29/h7,9-13,23,25-26,29,34-36H,8H2,1-6H3,(H2,32,39)(H,33,37)/t23-,25+,26-,29-/m1/s1
• InChIKey: YJQPYGGHQPGBLI-KGSXXDOSSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)c3ccc(c(c3)CC=C(C)C)O)O[C@H]4[C@@H]([C@@H]([C@H](C(O4)(C)C)OC)OC(=O)N)O
  CACTVS 3.370: CO[CH]1[CH](OC(N)=O)[CH](O)[CH](Oc2ccc3C(=C(NC(=O)c4ccc(O)c(CC=C(C)C)c4)C(=O)Oc3c2C)O)OC1(C)C
  ACDLabs 12.01: O=C(c1ccc(O)c(c1)C\C=C(/C)C)NC3=C(O)c4ccc(OC2OC(C(OC)C(OC(=O)N)C2O)(C)C)c(c4OC3=O)C
  CACTVS 3.370: CO[C@@H]1[C@@H](OC(N)=O)[C@@H](O)[C@H](Oc2ccc3C(=C(NC(=O)c4ccc(O)c(CC=C(C)C)c4)C(=O)Oc3c2C)O)OC1(C)C
  OpenEye OEToolkits 1.7.0: Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)c3ccc(c(c3)CC=C(C)C)O)OC4C(C(C(C(O4)(C)C)OC)OC(=O)N)O
• Formula: C31 H36 N2 O11
• Name: NOVOBIOCIN;
  4-Hydroxy-3-[4-hydroxy-3-(3-methylbut-2-enyl)benzamido]-8-methylcoumarin-7-yl 3-O-carbamoyl-5,5-di-C-methyl-alpha-l-lyxofuranoside
• ChEMBL: CHEMBL36506
• DrugBank: DB01051
• ZINC: ZINC000014879999
• PDB chain: 4urn Chain A Residue 2000

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4urn Structures of Kibdelomycin Bound to Staphylococcus Aureus Gyrb and Pare Showed a Novel U-Shaped Binding Mode.
• Resolution: 2.3 Å
• Binding residue (original residue number in PDB): N49 E53 R79 M81 P82 I96 R138
• Binding residue (residue number reindexed from 1): N33 E37 R63 M65 P66 I80 R103
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=4.46,IC50=35uM

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Thu Nov 28 09:57:51 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 = '4urn', asym_id = 'A', bs = 'BS01', title = 'Structures of Kibdelomycin Bound to Staphylococc...rb and Pare Showed a Novel U-Shaped Binding Mode.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4urn', asym_id='A', bs='BS01', title='Structures of Kibdelomycin Bound to Staphylococc...rb and Pare Showed a Novel U-Shaped Binding Mode.')

   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 = '0003677,0003918,0005524,0006265', uniprot = '', pdbid = '4urn', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003677,0003918,0005524,0006265', uniprot='', pdbid='4urn', 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>