Structure of PDB 6nr3 Chain D Binding Site BS01

Receptor Information

>6nr3 Chain D (length=854) Species: 59894 (Ficedula albicollis)

AAAAAAAAAAAAAAAAAAAAAAKYIRLSCDTDSETLYDLMTQHWHLKTPN
LVISVTKNFALKPRMRKIFSRLIYIAQSKGAWIFTGGTHYGLMKYIGEVV
RDNTISRSSEENVVAIKRDPLYCLDNNHTHLLLVTIEAKVRTQLEKYISE
RVIPESNYGGKIPIVCFAQGGGKETLKSINVAIKSKIPCVVVEGSGRIAD
VIASLVSSCVKESLLRFLPRTISRLSEEETESWIKWIKEVLESPHLLTVI
KIEEAGDEIVSNAISFALYKAFSTNEHDRDNWNGQLKLLLEWNQLDLASD
EIFTNDRNWESADLQDVMFTALVKDRPKFVRLFLENGLNLRKFLTTEVLR
ELYTNNFSSLVFKNLQIAKNSYNDALLTFVWKMVEDFRRPITRHPLQALF
IWSVLQNKKELSKVIWEQTRGCTLAALGASKLLKSMAKVKNDINAAGESE
ELANEYETRAVELFTECYSNDEDLAEQLLTYSCEAWGGSNCLELAVEARD
QQFIAQPGVQNFLSKQWYGEISRDTKNWKIILCLFFFPLIGCGFISFRKK
KLFLYYVSFFTSPFVVFSWNVIFYIAFLLLFAYVLLMDFQKEPTALEIIL
YVLVFILLCDEVRQWYMNGSKYFSDLWNVMDTLGIFYFIAGIVFRLHSWY
SGRVIFCLDYIVFTLRLIHIFTVSRNLGPKIIMLQRMMIDVFFFLFLFAV
WMVAFGVARQGILRWEWIFRSVIYEPYLAMFGEWITIPLVCIYMLSTNIL
LVNLLVAMFGNNDQVWKFQRFFLVQEYCSRLTIPFPFVIFAYIFMVMRKP
SVCCSRNEDNEILAWEAVMKENYLVKINTKAAAAAAAAAAAAAAAAAAAA
AAAA

Ligand information

• Ligand ID: KX7
• InChI: InChI=1S/C16H13N3O4/c20-15-7-2-1-6-14(15)18-9-8-13(17-16(18)21)11-4-3-5-12(10-11)19(22)23/h1-8,10,20H,9H2,(H,17,21)
• InChIKey: RCEFMOGVOYEGJN-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1ccc(c(c1)N2CC=C(NC2=O)c3cccc(c3)[N+](=O)[O-])O
  CACTVS 3.385: Oc1ccccc1N2CC=C(NC2=O)c3cccc(c3)[N+]([O-])=O
  ACDLabs 12.01: C1C=C(NC(N1c2ccccc2O)=O)c3cc(ccc3)[N+]([O-])=O
• Formula: C16 H13 N3 O4
• Name: Icilin;
  3-(2-hydroxyphenyl)-6-(3-nitrophenyl)-3,4-dihydropyrimidin-2(1H)-one
• ChEMBL: CHEMBL258405
• ZINC: ZINC000000620751
• PDB chain: 6nr3 Chain D Residue 1201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6nr3 Structural basis of cooling agent and lipid sensing by the cold-activated TRPM8 channel.
• Resolution: 3.4 Å
• Binding residue (original residue number in PDB): N741 V742 Y745 E782 D802 F838 R841 H844 I845 Y1004
• Binding residue (residue number reindexed from 1): N570 V571 Y574 E611 D631 F663 R666 H669 I670 Y777
• Annotation score: 1

Gene Ontology

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UnboundLocalError

Python 3.6.8: /usr/bin/python3 Mon Dec 2 10:07:25 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 = '6nr3', asym_id = 'D', bs = 'BS01', title = 'Structural basis of cooling agent and lipid sensing by the cold-activated TRPM8 channel.'

 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='6nr3', asym_id='D', bs='BS01', title='Structural basis of cooling agent and lipid sensing by the cold-activated TRPM8 channel.')

   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 = '0005216,0006811,0016020,0055085', uniprot = '', pdbid = '6nr3', asym_id = 'D'

 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005216,0006811,0016020,0055085', uniprot='', pdbid='6nr3', 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>