Structure of PDB 4mdt Chain D Binding Site BS02

Receptor Information
>4mdt Chain D (length=293) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDLNPPVDFPAD
AKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPEIPI
MDGSAAPFVYLLLDAGIDELNSAKKFVRIKETVRVEDGDKWAEFKPYNGF
SLDFTIDFNHPAIDSSNQRYAMNFSADAFMRQISRARTFGFMRDIEYLQS
RGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMCGHN
IIGAFTAYKSGHALNNKLLQAVLAKQEAWEYVTFQDDAELPLA
Ligand information
Ligand ID24G
InChIInChI=1S/C29H51N3O18P2/c1-2-3-4-5-6-7-8-9-10-11-17(34)14-21(36)48-26-22(30)28(47-18(15-33)24(26)38)49-52(43,44)50-51(41,42)45-16-19-23(37)25(39)27(46-19)32-13-12-20(35)31-29(32)40/h12-13,17-19,22-28,33-34,37-39H,2-11,14-16,30H2,1H3,(H,41,42)(H,43,44)(H,31,35,40)/t17-,18-,19-,22-,23-,24-,25-,26-,27-,28-/m1/s1
InChIKeyZFPNNOXCEDQJQS-SSVOXRMNSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC3OC(C(O)C(OC(=O)CC(O)CCCCCCCCCCC)C3N)CO)O)O
OpenEye OEToolkits 1.7.6CCCCCCCCCCC[C@H](CC(=O)O[C@@H]1[C@H]([C@H](O[C@@H]([C@H]1O)CO)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)N)O
CACTVS 3.385CCCCCCCCCCC[CH](O)CC(=O)O[CH]1[CH](N)[CH](O[CH](CO)[CH]1O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.7.6CCCCCCCCCCCC(CC(=O)OC1C(C(OC(C1O)CO)OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)N)O
CACTVS 3.385CCCCCCCCCCC[C@@H](O)CC(=O)O[C@@H]1[C@@H](N)[C@H](O[C@H](CO)[C@H]1O)O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O
FormulaC29 H51 N3 O18 P2
Nameuridine-5'-diphosphate-3-O-(R-3-hydroxymyristoyl)-glucosamine;
(2R,3R,4R,5S,6R)-3-amino-2-{[(R)-{[(S)-{[(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl (3R)-3-hydroxytetradecanoate
ChEMBL
DrugBank
ZINCZINC000096086573
PDB chain4mdt Chain D Residue 402 [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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PDB4mdt Structure of the Bacterial Deacetylase LpxC Bound to the Nucleotide Reaction Product Reveals Mechanisms of Oxyanion Stabilization and Proton Transfer.
Resolution2.59 Å
Binding residue
(original residue number in PDB)		L18 K143 I159 D160 F161 F192 F194 M195 I198 G210 S211 A215 K239 K262 G264 H265
Binding residue
(residue number reindexed from 1)		L15 K140 I156 D157 F158 F189 F191 M192 I195 G207 S208 A212 K236 K259 G261 H262
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 22 16:22:57 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 = '4mdt', asym_id = 'D', bs = 'BS02', title = 'Structure of the Bacterial Deacetylase LpxC Boun...s of Oxyanion Stabilization and Proton Transfer. '
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4mdt', asym_id='D', bs='BS02', title='Structure of the Bacterial Deacetylase LpxC Boun...s of Oxyanion Stabilization and Proton Transfer. ')
   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 = '0008759,0009245', uniprot = '', pdbid = '4mdt', asym_id = 'D'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0008759,0009245', uniprot='', pdbid='4mdt', 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>