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BioLiP

Structure of PDB 5znj Chain A Binding Site BS01

Receptor Information
>5znj Chain A (length=563) 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
NDIKLKSYFGTDNIELATQDEIVNLVGSLGPVIDKEIKIYADNFVQDLNN
LVVGANEDGYHLINVNVGRDFNVDEYGDFRFILEGEKLSDGSGVAHFAEG
IEVGQVFKLGTKYSESMNATFLDNQGKAQPLIMGCYGIGISRTLSAIVEQ
NHDDNGIVWPKSVTPFDLHLISINPKKDDQRELADALYAEFNTKFDVLYD
DRQERAGVKFNDADLIGLPLRIVVGKRASEGIVEVKERLTGDSEEVHIDD
LMTVITNKYDNLK
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain5znj Chain A Residue 601 [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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PDB5znj Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase.
Resolution1.84 Å
Binding residue
(original residue number in PDB)		R140 E142 R151 G152 F155 M157 E406 V407 G408 G443 R446
Binding residue
(residue number reindexed from 1)		R140 E142 R151 G152 F155 M157 E402 V403 G404 G439 R442
Annotation score3
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Tue May 13 02:57:13 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 = '5znj', asym_id = 'A', bs = 'BS01', 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='BS01', 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 = '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')
    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>