Structure of PDB 4pnw Chain B Binding Site BS01

Receptor Information

>4pnw Chain B (length=364) Species: 1403831 (Escherichia coli str. K-12 substr. MC4100)

MKFTVEREHLLKPLQQVSGPLGGRPTLPILGNLLLQVADGTLSLTGTDLE
MEMVARVALVQPHEPGATTVPARKFFDICRGLPEGAEIAVQLEGERMLVR
SGRSRFSLSTLPAADFPNLDDWQSEVEFTLPQATMKRLIEATQFSMAHQD
VRYYLNGMLFETEGEELRTVATDGHRLAVCSMPIGQSLPSHSVIVPRKGV
IELMRMLDGGDNPLRVQIGSNNIRAHVGDFIFTSKLVDGRFPDYRRVLPK
NPDKHLEAGCDLLKQAFARAAILSNEKFRGVRLYVSENQLKITANNPEQE
EAEEILDVTYSGAEMEIGFNVSYVLDVLNALKCENVRMMLTDSVSSVQIE
DAASQSAAYVVMPM

Ligand information

• Ligand ID: 2VM
• InChI: InChI=1S/C24H23BrN2O5/c25-16-7-9-20-18(12-16)17-8-6-15(23(29)30)11-21(17)27(20)13-22(28)26-19(24(31)32)10-14-4-2-1-3-5-14/h1-5,7,9,12,15,19H,6,8,10-11,13H2,(H,26,28)(H,29,30)(H,31,32)/t15-,19+/m1/s1
• InChIKey: VVKCJZLVMZAHBK-BEFAXECRSA-N
• SMILES:
  CACTVS 3.385: OC(=O)[C@@H]1CCc2c(C1)n(CC(=O)N[C@@H](Cc3ccccc3)C(O)=O)c4ccc(Br)cc24
  CACTVS 3.385: OC(=O)[CH]1CCc2c(C1)n(CC(=O)N[CH](Cc3ccccc3)C(O)=O)c4ccc(Br)cc24
  ACDLabs 12.01: O=C(O)C(NC(=O)Cn1c3c(c2c1CC(C(=O)O)CC2)cc(Br)cc3)Cc4ccccc4
  OpenEye OEToolkits 1.7.6: c1ccc(cc1)CC(C(=O)O)NC(=O)Cn2c3ccc(cc3c4c2CC(CC4)C(=O)O)Br
  OpenEye OEToolkits 1.7.6: c1ccc(cc1)C[C@@H](C(=O)O)NC(=O)Cn2c3ccc(cc3c4c2C[C@@H](CC4)C(=O)O)Br
• Formula: C24 H23 Br N2 O5
• Name: (2R)-6-bromo-9-(2-{[(1S)-1-carboxy-2-phenylethyl]amino}-2-oxoethyl)-2,3,4,9-tetrahydro-1H-carbazole-2-carboxylic acid
• ChEMBL: CHEMBL3577290
• ZINC: ZINC000098208319
• PDB chain: 4pnw Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4pnw Bacterial Sliding Clamp Inhibitors that Mimic the Sequential Binding Mechanism of Endogenous Linear Motifs.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): Y154 D173 G174 H175 R176 L177 V360 M362
• Binding residue (residue number reindexed from 1): Y154 D173 G174 H175 R176 L177 V360 M362
• Annotation score: 1
• Binding affinity: PDBbind-CN: -logKd/Ki=5.05,Kd=9uM

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Fri Nov 22 16:55:58 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 = '4pnw', asym_id = 'B', bs = 'BS01', title = 'Bacterial Sliding Clamp Inhibitors that Mimic th...al Binding Mechanism of Endogenous Linear Motifs.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4pnw', asym_id='B', bs='BS01', title='Bacterial Sliding Clamp Inhibitors that Mimic th...al Binding Mechanism of Endogenous Linear Motifs.')

   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 = '0003677,0003887,0006260,0008408,0009360', uniprot = '', pdbid = '4pnw', asym_id = 'B'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003677,0003887,0006260,0008408,0009360', uniprot='', pdbid='4pnw', asym_id='B')

    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>