Structure of PDB 8dl2 Chain B Binding Site BS06

Receptor Information
>8dl2 Chain B (length=712) Species: 411476 (Bacteroides ovatus ATCC 8483) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
LHDGFNFDPAIPKADEPLTITFKAPEGSNFYGYADDLYLHSGTGANWTGA
PTWGDNQNKYRLKKTKDNVWSITLSSSIRHFYSVAPSTPLQTINLIVRDA
EGSQQTYDYATLVEDSQNGFIWEEPQKAPLPISGEEKEGIHIHSATSIML
VLYDKDSQGGHKDCVFVTGNFNNWKLDSRYMMKYDETNHCWWITLEELTA
ETQFQYFVYSASDGGTYLCDPYCEQALEKGVDTNFPTGAQAPYVSVVSTN
PQPYQWSAGEFEMKNKENPVIYELLLRDFTSSGNLAGAMEKLPYLKELGI
DAIELMPVQEFAGNDSWGYNTGLYFALDASYGTQNEYKAFIDACHQNGIA
VIFDVVYNHTNNDNPFARMYWDTFNNRPSTKNPWLNAVTPHQKYVFSPDD
FNHTSEQTKAFVKRNLKYLLDTYHIDGFRFDFTKGFTQKQTTGDDDLAAT
DPARVSVLKEYYEAVKAVKEDAMVTMEHFCANEETTLATEGIHFWRNMNH
SYCQSAMGWKDNSDFSGLYDTTRPNQFVGYMESHDEERCAYKQIEYGNGA
LKTNLSERLKQLSSNAAFFFTVPGPKMLWQFGEMGYDISIDENGRTGKKP
VLWEYQTERKSLVDIYTKLITLRTTHSDLFNASSQFTWKVSYNDWDNGRT
LTLKAVNGKQLHVYANFTNASIDYTIPEGTWYLYLENGNPVEGEKKISVP
AHEFRLYTNFAE
Ligand information
Ligand IDAC1
InChIInChI=1S/C13H23NO8/c1-4-7(10(18)12(20)13(21)22-4)14-6-2-5(3-15)8(16)11(19)9(6)17/h2,4,6-21H,3H2,1H3/t4-,6+,7-,8-,9+,10+,11+,12-,13+/m1/s1
InChIKeyRBZIIHWPZWOIDU-ZCGMLSCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC1C(C(C(C(O1)O)O)O)NC2C=C(C(C(C2O)O)O)CO
CACTVS 3.341C[CH]1O[CH](O)[CH](O)[CH](O)[CH]1N[CH]2C=C(CO)[CH](O)[CH](O)[CH]2O
OpenEye OEToolkits 1.5.0C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)N[C@H]2C=C([C@H]([C@@H]([C@H]2O)O)O)CO
ACDLabs 10.04OC2C(NC1C=C(CO)C(O)C(O)C1O)C(OC(O)C2O)C
CACTVS 3.341C[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1N[C@H]2C=C(CO)[C@@H](O)[C@H](O)[C@H]2O
FormulaC13 H23 N O8
Name4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose;
6-METHYL-5-(4,5,6-TRIHYDROXY-3-HYDROXYMETHYL-CYCLOHEX-2-ENYLAMINO)-TETRAHYDRO-PYRAN-2,3,4-TRIOL;
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucose;
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-D-glucose;
4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-glucose
ChEMBL
DrugBankDB02218
ZINCZINC000058638973
PDB chain8dl2 Chain M Residue 3 [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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PDB8dl2 BoGH13A Sus from Bacteroides ovatus represents a novel alpha-amylase used for Bacteroides starch breakdown in the human gut.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		W363 Y365 F442 D477 F478 E523 H580 D581
Binding residue
(residue number reindexed from 1)		W317 Y319 F396 D431 F432 E477 H534 D535
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Mon Nov 25 14:04:51 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 = '8dl2', asym_id = 'B', bs = 'BS06', title = 'BoGH13A Sus from Bacteroides ovatus represents a...or Bacteroides starch breakdown in the human gut.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='8dl2', asym_id='B', bs='BS06', title='BoGH13A Sus from Bacteroides ovatus represents a...or Bacteroides starch breakdown in the human gut.')
   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 = '0005975', uniprot = '', pdbid = '8dl2', asym_id = 'B'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0005975', uniprot='', pdbid='8dl2', 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>