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BioLiP

Structure of PDB 5znk Chain A Binding Site BS03

Receptor Information
>5znk Chain A (length=562) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKQSKVFIPTMRDVPSEAEAQSHRLLLKSGLIKQSTSGIYSYLPLATRVL
NNITAIVRQEMERIDSVEILMPALQQAELWEESGRWGAYGPELMRLQDRH
GRQFALGPTHEELVTSIVRNELKSYKQLPMTLFQIQSKFRDEKRPRFGLL
RGREFIMKDAYSFHADEASLDQTYQDMYQAYSRIFERVGINARPVVADSG
AIGGSHTHEFMALSAIGEDTIVYSKESDYTANIEKAEVVYEPNHKHSTVQ
PLEKIETPNVKTAQELADFLGRPVDEIAKTMIFKVDGEYIMVLVRGHHEI
NDIKLKSYFGTDNIELATQDEIVNLVSLGPVIDKEIKIYADNFVQDLNNL
VVGANEDGYHLINVNVGRDFNVDEYGDFRFILEGEKLSDGSGVAHFAEGI
EVGQVFKLGTKYSESMNATFLDNQGKAQPLIMGCYGIGISRTLSAIVEQN
HDDNGIVWPKSVTPFDLHLISINPKKDDQRELADALYAEFNTKFDVLYDD
RQERAGVKFNDADLIGLPLRIVVGKRASEGIVEVKERLTGDSEEVHIDDL
MTVITNKYDNLK
Ligand information
Ligand ID9G3
InChIInChI=1S/C16H17ClFN3O2/c17-13-7-15-12(6-14(13)18)16(23)21(9-20-15)8-11(22)5-10-3-1-2-4-19-10/h6-7,9-10,19H,1-5,8H2/t10-/m0/s1
InChIKeyLZMOBHASNVDDQN-JTQLQIEISA-N
SMILES
SoftwareSMILES
CACTVS 3.385Fc1cc2C(=O)N(CC(=O)C[CH]3CCCCN3)C=Nc2cc1Cl
OpenEye OEToolkits 2.0.6c1c2c(cc(c1F)Cl)N=CN(C2=O)CC(=O)C[C@@H]3CCCCN3
CACTVS 3.385Fc1cc2C(=O)N(CC(=O)C[C@@H]3CCCCN3)C=Nc2cc1Cl
ACDLabs 12.01c1(F)c(Cl)cc2c(c1)C(=O)N(C=N2)CC(=O)CC3NCCCC3
OpenEye OEToolkits 2.0.6c1c2c(cc(c1F)Cl)N=CN(C2=O)CC(=O)CC3CCCCN3
FormulaC16 H17 Cl F N3 O2
Name7-chloro-6-fluoro-3-{2-oxo-3-[(2S)-piperidin-2-yl]propyl}quinazolin-4(3H)-one
ChEMBLCHEMBL5178546
DrugBank
ZINC
PDB chain5znk Chain A Residue 605 [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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PDB5znk Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase.
Resolution2.07 Å
Binding residue
(original residue number in PDB)		W80 R85 Y89 E92 L93 P108 T109 E111 R140 M157 Y161 F411 G441
Binding residue
(residue number reindexed from 1)		W80 R85 Y89 E92 L93 P108 T109 E111 R140 M157 Y161 F406 G436
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Tue May 13 02:46:21 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>()
   1701     title=pdb2title(pdbid)
   1702     if bs.startswith("BS"):
=> 1703         pubmed,uniprot=display_interaction(pdbid,asym_id,bs,title)
   1704     else:
   1705         if lig3:
pubmed = '', uniprot = '', display_interaction = <function display_interaction>, pdbid = '5znk', asym_id = 'A', bs = 'BS03', title = 'Structure-Guided Design of Halofuginone Derivati...ibitors Against Bacterial Prolyl-tRNA Synthetase.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5znk', asym_id='A', bs='BS03', title='Structure-Guided Design of Halofuginone Derivati...ibitors Against Bacterial Prolyl-tRNA Synthetase.')
   1326         display_ec(ec,csaOrig,csaRenu)
   1327     if go:
=> 1328         display_go(go,uniprot,pdbid,asym_id)
   1329     return pubmed,uniprot
   1330 
global display_go = <function display_go>, go = '0000166,0002161,0004812,0004827,0005524,0005737,0006418,0006433', uniprot = '', pdbid = '5znk', asym_id = 'A'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0000166,0002161,0004812,0004827,0005524,0005737,0006418,0006433', uniprot='', pdbid='5znk', asym_id='A')
    484         '''.replace("$namespace_link",namespace_link
    485           ).replace("$namespace",namespace
=>  486           ).replace("$uniprot",u
    487         ))
    488         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>