Structure of PDB 3nix Chain D Binding Site BS01

Receptor Information

>3nix Chain D (length=403) Species: 269798 (Cytophaga hutchinsonii ATCC 33406)

KVDVLVIGAGPAGTVAASLVNKSGFKVKIVEKQKFPRFVIGESLLPRCME
HLDEAGFLDAVKAQGFQQKFGAKFVRGKEIADFNFSDQFSNGWNWTWQVP
RGNFDKTLADEAARQGVDVEYEVGVTDIKFFGTDSVTTIEDINGNKREIE
ARFIIDASGYGRVIPRMFGLDKPSGFESRRTLFTHIKDVKRPVGNRITAV
VHKPKVWIWVIPFSNGNTSVGFVGEPSYFDEYTGTPEERMRAMIANEGHI
AERFKSEEFLFEPRTIEGYAISASKLYGDGFVLTGNATEFLDPIFSSGAT
FAMESGSKGGKLAVQFLKGEEVNWEKDFVEHMMQGIDTFRSFVTGWYDGT
LHAVFFAKNPDPDHKRMICSVLAGYVWDKNNPFVKKHNTILKTLAKVIQM
GEE

Ligand information

• Ligand ID: FAD
• InChI: InChI=1S/C27H33N9O15P2/c1-10-3-12-13(4-11(10)2)35(24-18(32-12)25(42)34-27(43)33-24)5-14(37)19(39)15(38)6-48-52(44,45)51-53(46,47)49-7-16-20(40)21(41)26(50-16)36-9-31-17-22(28)29-8-30-23(17)36/h3-4,8-9,14-16,19-21,26,37-41H,5-7H2,1-2H3,(H,44,45)(H,46,47)(H2,28,29,30)(H,34,42,43)/t14-,15+,16+,19-,20+,21+,26+/m0/s1
• InChIKey: VWWQXMAJTJZDQX-UYBVJOGSSA-N
• SMILES:
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P@](O)(=O)O[P@@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6c(N)ncnc56)c2cc1C
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5ncnc6N)O)O)O)O)O
  OpenEye OEToolkits 1.5.0: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](CO[P@@](=O)(O)O[P@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5ncnc6N)O)O)O)O)O
  CACTVS 3.341: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6c(N)ncnc56)c2cc1C
  ACDLabs 10.04: O=C2C3=Nc1cc(c(cc1N(C3=NC(=O)N2)CC(O)C(O)C(O)COP(=O)(O)OP(=O)(O)OCC6OC(n5cnc4c(ncnc45)N)C(O)C6O)C)C
• Formula: C27 H33 N9 O15 P2
• Name: FLAVIN-ADENINE DINUCLEOTIDE
• ChEMBL: CHEMBL1232653
• DrugBank: DB03147
• ZINC: ZINC000008215434
• PDB chain: 3nix Chain D Residue 504

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3nix Crystal structure of flavoprotein/dehydrogenase from Cytophaga hutchinsonii.
• Resolution: 2.6 Å
• Binding residue (original residue number in PDB): G14 P15 A16 V34 E35 K36 Q37 R41 I44 G45 S47 R105 V129 S162 G163 Y164 V167 N295 F299 P302 S305 G307 A308 A311
• Binding residue (residue number reindexed from 1): G10 P11 A12 V30 E31 K32 Q33 R37 I40 G41 S43 R101 V125 S158 G159 Y160 V163 N286 F290 P293 S296 G298 A299 A302
• Annotation score: 4

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Thu Feb 20 05:48:19 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>()

   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 = '3nix', asym_id = 'D', bs = 'BS01', title = 'Crystal structure of flavoprotein/dehydrogenase from Cytophaga hutchinsonii.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='3nix', asym_id='D', bs='BS01', title='Crystal structure of flavoprotein/dehydrogenase from Cytophaga hutchinsonii.')

   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 = '0071949', uniprot = '', pdbid = '3nix', asym_id = 'D'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0071949', uniprot='', pdbid='3nix', asym_id='D')

    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>