Structure of PDB 5znj Chain A Binding Site BS02

Receptor Information

>5znj Chain A (length=563) Species: 1280 (Staphylococcus aureus)

MKQSKVFIPTMRDVPSEAEAQSHRLLLKSGLIKQSTSGIYSYLPLATRVL
NNITAIVRQEMERIDSVEILMPALQQAELWEESGRWGAYGPELMRLQDRH
GRQFALGPTHEELVTSIVRNELKSYKQLPMTLFQIQSKFRDEKRPRFGLL
RGREFIMKDAYSFHADEASLDQTYQDMYQAYSRIFERVGINARPVVADSG
AIGGSHTHEFMALSAIGEDTIVYSKESDYTANIEKAEVVYEPNHKHSTVQ
PLEKIETPNVKTAQELADFLGRPVDEIAKTMIFKVDGEYIMVLVRGHHEI
NDIKLKSYFGTDNIELATQDEIVNLVGSLGPVIDKEIKIYADNFVQDLNN
LVVGANEDGYHLINVNVGRDFNVDEYGDFRFILEGEKLSDGSGVAHFAEG
IEVGQVFKLGTKYSESMNATFLDNQGKAQPLIMGCYGIGISRTLSAIVEQ
NHDDNGIVWPKSVTPFDLHLISINPKKDDQRELADALYAEFNTKFDVLYD
DRQERAGVKFNDADLIGLPLRIVVGKRASEGIVEVKERLTGDSEEVHIDD
LMTVITNKYDNLK

Ligand information

• Ligand ID: HFG
• InChI: InChI=1S/C16H17BrClN3O3/c17-11-6-13-10(5-12(11)18)16(24)21(8-20-13)7-9(22)4-14-15(23)2-1-3-19-14/h5-6,8,14-15,19,23H,1-4,7H2/t14-,15+/m1/s1
• InChIKey: LVASCWIMLIKXLA-CABCVRRESA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1c2c(cc(c1Cl)Br)N=CN(C2=O)CC(=O)CC3C(CCCN3)O
  OpenEye OEToolkits 1.7.6: c1c2c(cc(c1Cl)Br)N=CN(C2=O)CC(=O)C[C@@H]3[C@H](CCCN3)O
  CACTVS 3.370: O[C@H]1CCCN[C@@H]1CC(=O)CN2C=Nc3cc(Br)c(Cl)cc3C2=O
  CACTVS 3.370: O[CH]1CCCN[CH]1CC(=O)CN2C=Nc3cc(Br)c(Cl)cc3C2=O
  ACDLabs 12.01: Brc3c(Cl)cc1c(N=CN(C1=O)CC(=O)CC2NCCCC2O)c3
• Formula: C16 H17 Br Cl N3 O3
• Name: 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one;
  Halofuginone
• ChEMBL: CHEMBL1199540
• DrugBank: DB04866
• ZINC: ZINC000005784191
• PDB chain: 5znj Chain A Residue 602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5znj Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase.
• Resolution: 1.84 Å
• Binding residue (original residue number in PDB): R85 Y89 E92 L93 P108 T109 E111 R140 Y161 Y440 G441
• Binding residue (residue number reindexed from 1): R85 Y89 E92 L93 P108 T109 E111 R140 Y161 Y436 G437
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Wed Nov 27 02:06:08 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 = '5znj', asym_id = 'A', bs = 'BS02', title = 'Structure-Guided Design of Halofuginone Derivati...ibitors Against Bacterial Prolyl-tRNA Synthetase.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5znj', asym_id='A', bs='BS02', title='Structure-Guided Design of Halofuginone Derivati...ibitors Against Bacterial Prolyl-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 = '0000166,0002161,0004812,0004827,0005524,0005737,0006418,0006433', uniprot = '', pdbid = '5znj', asym_id = 'A'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000166,0002161,0004812,0004827,0005524,0005737,0006418,0006433', uniprot='', pdbid='5znj', 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>