Structure of PDB 5znk Chain A Binding Site BS01

Receptor Information

>5znk Chain A (length=562) Species: 1280 (Staphylococcus aureus)

MKQSKVFIPTMRDVPSEAEAQSHRLLLKSGLIKQSTSGIYSYLPLATRVL
NNITAIVRQEMERIDSVEILMPALQQAELWEESGRWGAYGPELMRLQDRH
GRQFALGPTHEELVTSIVRNELKSYKQLPMTLFQIQSKFRDEKRPRFGLL
RGREFIMKDAYSFHADEASLDQTYQDMYQAYSRIFERVGINARPVVADSG
AIGGSHTHEFMALSAIGEDTIVYSKESDYTANIEKAEVVYEPNHKHSTVQ
PLEKIETPNVKTAQELADFLGRPVDEIAKTMIFKVDGEYIMVLVRGHHEI
NDIKLKSYFGTDNIELATQDEIVNLVSLGPVIDKEIKIYADNFVQDLNNL
VVGANEDGYHLINVNVGRDFNVDEYGDFRFILEGEKLSDGSGVAHFAEGI
EVGQVFKLGTKYSESMNATFLDNQGKAQPLIMGCYGIGISRTLSAIVEQN
HDDNGIVWPKSVTPFDLHLISINPKKDDQRELADALYAEFNTKFDVLYDD
RQERAGVKFNDADLIGLPLRIVVGKRASEGIVEVKERLTGDSEEVHIDDL
MTVITNKYDNLK

Ligand information

• Ligand ID: ANP
• InChI: InChI=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
• InChIKey: PVKSNHVPLWYQGJ-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.7.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
  CACTVS 3.370: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
  CACTVS 3.370: Nc1ncnc2n(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 12.01: O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  OpenEye OEToolkits 1.7.0: c1nc(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
• Formula: C10 H17 N6 O12 P3
• Name: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
• ChEMBL: CHEMBL1230989
• ZINC: ZINC000008660410
• PDB chain: 5znk Chain A Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5znk Structure-Guided Design of Halofuginone Derivatives as ATP-Aided Inhibitors Against Bacterial Prolyl-tRNA Synthetase.
• Resolution: 2.07 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 E401 V402 G403 G438 R441
• Annotation score: 3

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Tue Nov 26 22:35:59 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 = '5znk', 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='5znk', asym_id='A', bs='BS01', 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 = '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')

    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>