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BioLiP

Structure of PDB 5o9f Chain B Binding Site BS03

Receptor Information
>5o9f Chain B (length=346) Species: 1925550 (Rhodococcus sp. M8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MKAVQYTEIGSEPVVVDIPTPTPGPGEILLKVTAAGLCYSDISVMDMPAA
QYAYGLPLTLGHEGVGTVAELGEGVTGFGVGDAVAVYGPWGCGACHACAR
GRENYCTRAADLGITPPGLGSPGSMAEYMIVDSARHLVPIGDLDPVAAAP
LTDAGLTPYHAISRVLPLLGPGSTAVVIGVGGLGHVGIQILRAVSAARVI
AVDLDDDRLALAREVGADAAVKSGAGAADAIRELTGGQGATAVFDFVGAQ
STIDTAQQVVAVDGHISVVGIHAGAHAKVGFFMIPFGASVVTPFAGTRSE
LMEVVALARAGRLDIHTETFTLDEGPAAYRRLREGSIRGRGVVVPT
Ligand information
Ligand IDNAD
InChIInChI=1S/C21H27N7O14P2/c22-17-12-19(25-7-24-17)28(8-26-12)21-16(32)14(30)11(41-21)6-39-44(36,37)42-43(34,35)38-5-10-13(29)15(31)20(40-10)27-3-1-2-9(4-27)18(23)33/h1-4,7-8,10-11,13-16,20-21,29-32H,5-6H2,(H5-,22,23,24,25,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1
InChIKeyBAWFJGJZGIEFAR-NNYOXOHSSA-N
SMILES
SoftwareSMILES
CACTVS 3.341NC(=O)c1ccc[n+](c1)[C@@H]2O[C@H](CO[P]([O-])(=O)O[P@](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
CACTVS 3.341NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)([O-])O[P@@](=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O)O)O)C(=O)N
FormulaC21 H27 N7 O14 P2
NameNICOTINAMIDE-ADENINE-DINUCLEOTIDE
ChEMBLCHEMBL1234613
DrugBankDB14128
ZINC
PDB chain5o9f Chain B Residue 503 [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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PDB5o9f Relaxation of nonproductive binding and increased rate of coenzyme release in an alcohol dehydrogenase increases turnover with a nonpreferred alcohol enantiomer.
Resolution1.64 Å
Binding residue
(original residue number in PDB)		C38 Y39 S40 D153 T157 V180 G181 G182 L183 D203 L204 R208 S223 F246 V247 T252 V269 G270 I271 F294 R340
Binding residue
(residue number reindexed from 1)		C38 Y39 S40 D153 T157 V180 G181 G182 L183 D203 L204 R208 S223 F246 V247 T252 V269 G270 I271 F294 R340
Annotation score4
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Mon May 12 16:27:05 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 = '5o9f', asym_id = 'B', bs = 'BS03', title = 'Relaxation of nonproductive binding and increase...turnover with a nonpreferred alcohol enantiomer. '
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='5o9f', asym_id='B', bs='BS03', title='Relaxation of nonproductive binding and increase...turnover with a nonpreferred alcohol enantiomer. ')
   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 = '0008270,0016491', uniprot = '', pdbid = '5o9f', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0008270,0016491', uniprot='', pdbid='5o9f', asym_id='B')
    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>