Structure of PDB 4r3w Chain B Binding Site BS01

Receptor Information

>4r3w Chain B (length=347) Species: 406563 (Streptococcus pneumoniae SP23-BS72)

GYTVAVVGATGAVGAQMIKMLEESTLPIDKIRYLASARSAGKSLKFKDQD
ITIEETTETAFEGVDIALFSAGSSTSAKYAPYAVKAGVVVVDNTSYFRQN
PDVPLVVPEVNAHALDAHNGIIACPNCSTIQMMVALEPVRQKWGLDRIIV
STYQAVSGAGMGAILETQRELREVLNDGVKPCDLHAEILPSGGDKKHYPI
AFNALPQIDVFTDNDYTYEEMKMTKETKKIMEDDSIAVSATCVRIPVLSA
HSESVYIETKEVAPIEEVKAAIAAFPGAVLEDDVAHQIYPQAINAVGSRD
TFVGRIRKDLDAEKGIHMWVVSDNLLKGAAWNSVQIAETLHERGLVR

Ligand information

• Ligand ID: A2P
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(25-27(20,21)22)6(16)4(24-10)1-23-26(17,18)19/h2-4,6-7,10,16H,1H2,(H2,11,12,13)(H2,17,18,19)(H2,20,21,22)/t4-,6-,7-,10-/m1/s1
• InChIKey: AEOBEOJCBAYXBA-KQYNXXCUSA-N
• SMILES:
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O[P](O)(O)=O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)OP(=O)(O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O[P](O)(O)=O
  ACDLabs 10.04: O=P(O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(OP(=O)(O)O)C3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)OP(=O)(O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-2'-5'-DIPHOSPHATE
• ChEMBL: CHEMBL1161861
• DrugBank: DB02098
• ZINC: ZINC000004096223
• PDB chain: 4r3w Chain B Residue 408

Receptor-Ligand Complex Structure

Structure summary

• PDB: 4r3w A cautionary tale of structure-guided inhibitor development against an essential enzyme in the aspartate-biosynthetic pathway.
• Resolution: 1.91 Å
• Binding residue (original residue number in PDB): G9 T11 G12 A13 A36 S37 S40 A72 T76 G161
• Binding residue (residue number reindexed from 1): G8 T10 G11 A12 A35 S36 S39 A71 T75 G160
• Annotation score: 3
• Binding affinity: MOAD: Ki=1mM

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Sun Nov 24 21:32:42 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 = '4r3w', asym_id = 'B', bs = 'BS01', title = 'A cautionary tale of structure-guided inhibitor ...ial enzyme in the aspartate-biosynthetic pathway.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4r3w', asym_id='B', bs='BS01', title='A cautionary tale of structure-guided inhibitor ...ial enzyme in the aspartate-biosynthetic pathway.')

   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 = '0004073,0008652,0009086,0009088,0009089,0009097,0016620,0046983,0050661,0051287', uniprot = '', pdbid = '4r3w', asym_id = 'B'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0004073,0008652,0009086,0009088,0009089,0009097,0016620,0046983,0050661,0051287', uniprot='', pdbid='4r3w', 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>