Structure of PDB 4f2w Chain B Binding Site BS01

Receptor Information
>4f2w Chain B (length=237) Species: 904139 (Salmonella enterica subsp. enterica serovar Choleraesuis str. SCSA50) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LVPRGSHMKIGIIGAMEEEVTLLRDKIDNRQTITLGGCEIYTGQLNGTEV
ALLKSGIGKVAAALGATLLLEHCKPDVIINTGSAGGLASTLKVGDIVVSD
ETRYHDADVTAFGYEYGQLPGCPAGFKADDKLIAAAESCIRELNLNAVRG
LIVSGDAFINGSVGLAKIRHNFPDAVAVEMEATAIAHVCHNFNVPFVVVR
AISDVADQQSHLSFDEFLAVAAKQSTLMVETLVQKLA
Ligand information
Ligand IDTDI
InChIInChI=1S/C13H19N5OS/c1-20-6-9-4-18(5-10(9)19)3-8-2-15-12-11(8)16-7-17-13(12)14/h2,7,9-10,15,19H,3-6H2,1H3,(H2,14,16,17)/t9-,10+/m1/s1
InChIKeyNTHMDFGHOCNNOE-ZJUUUORDSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CSCC1CN(CC1O)Cc2c[nH]c3c2ncnc3N
CACTVS 3.341CSC[CH]1CN(C[CH]1O)Cc2c[nH]c3c(N)ncnc23
OpenEye OEToolkits 1.5.0CSC[C@H]1C[N@](C[C@@H]1O)Cc2c[nH]c3c2ncnc3N
CACTVS 3.341CSC[C@H]1CN(C[C@@H]1O)Cc2c[nH]c3c(N)ncnc23
ACDLabs 10.04S(C)CC3CN(Cc2cnc1c2ncnc1N)CC3O
FormulaC13 H19 N5 O S
Name(3R,4S)-1-[(4-AMINO-5H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]-4-[(METHYLSULFANYL)METHYL]PYRROLIDIN-3-OL;
(3R,4S)-1-[9-DEAZAADENIN-9-YL)METHYL]-3-HYDROXY-4-(METHYLTHIOMETHYL)PYRROLIDINE
ChEMBLCHEMBL405346
DrugBankDB08606
ZINCZINC000011686540
PDB chain4f2w Chain B Residue 301 [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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PDB4f2w Crystal structure of 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase from Salmonella enterica with methyl-thio-DADMe-Immucillin-A
Resolution2.0 Å
Binding residue
(original residue number in PDB)		I50 S76 A77 G78 F151 I152 E172 M173 E174 D197 F207
Binding residue
(residue number reindexed from 1)		I57 S83 A84 G85 F158 I159 E179 M180 E181 D204 F214
Annotation score1
Binding affinityMOAD: Ki=5pM
PDBbind-CN: -logKd/Ki=11.30,Ki=5.0pM
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Thu Nov 28 06:10:56 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 = '4f2w', asym_id = 'B', bs = 'BS01', title = "Crystal structure of 5'-methylthioadenosine/S-ad...lla enterica with methyl-thio-DADMe-Immucillin-A "
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4f2w', asym_id='B', bs='BS01', title="Crystal structure of 5'-methylthioadenosine/S-ad...lla enterica with methyl-thio-DADMe-Immucillin-A ")
   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 = '0003824,0008782,0008930,0009116,0009164,0019509', uniprot = '', pdbid = '4f2w', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0003824,0008782,0008930,0009116,0009164,0019509', uniprot='', pdbid='4f2w', 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>