Structure of PDB 4oca Chain A Binding Site BS01

Receptor Information
>4oca Chain A (length=363) Species: 90371 (Salmonella enterica subsp. enterica serovar Typhimurium) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SDFLPFSRPAMGAEELAAVKTVLDSGWITTGPKNQELEAAFCRLTGNQYA
VAVSSATAGMHIALMALGIGEGDEVITPSMTWVSTLNMIVLLGANPVMVD
VDRDTLMVTPEHIEAAITPQTKAIIPVHYAGAPADLDAIYALGERYGIPV
IEDAAHATGTSYKGRHIGARGTAIFSFHAIANITCAEGGIVVTDNPQFAD
KLRSLKFHGLGAEVLAPGYKYNLPDLNAAIALAQLQKLDALNARRAAIAA
QYHQAMADLPFQPLSLPSWEHIHAWHLFIIRVDEARCGITRDALMASLKT
KGIGTGLHFRAAHTQKYYRERFPTLTLPDTEWNSERICSLPLFPDMTESD
FDRVITALHQIAG
Ligand information
Ligand ID2QR
InChIInChI=1S/C22H33N4O20P3/c1-9-15(28)11(10(4-23-9)6-42-47(34,35)36)5-24-12-7-41-21(19(32)16(12)29)45-49(39,40)46-48(37,38)43-8-13-17(30)18(31)20(44-13)26-3-2-14(27)25-22(26)33/h2-4,12-13,16-21,24,28-32H,5-8H2,1H3,(H,37,38)(H,39,40)(H,25,27,33)(H2,34,35,36)/t12-,13+,16-,17+,18+,19+,20+,21+/m0/s1
InChIKeySNDXWZNPMTZYQI-LLAQWDROSA-N
SMILES
SoftwareSMILES
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(CN[C@H]2CO[C@H](O[P](O)(=O)O[P](O)(=O)OC[C@H]3O[C@H]([C@H](O)[C@@H]3O)N4C=CC(=O)NC4=O)[C@H](O)[C@H]2O)c1O
OpenEye OEToolkits 1.7.6Cc1c(c(c(cn1)COP(=O)(O)O)CNC2COC(C(C2O)O)OP(=O)(O)OP(=O)(O)OCC3C(C(C(O3)N4C=CC(=O)NC4=O)O)O)O
CACTVS 3.385Cc1ncc(CO[P](O)(O)=O)c(CN[CH]2CO[CH](O[P](O)(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)N4C=CC(=O)NC4=O)[CH](O)[CH]2O)c1O
ACDLabs 12.01O=C1C=CN(C(=O)N1)C2OC(C(O)C2O)COP(=O)(OP(=O)(OC4OCC(NCc3c(cnc(c3O)C)COP(=O)(O)O)C(O)C4O)O)O
OpenEye OEToolkits 1.7.6Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@H]2CO[C@@H]([C@@H]([C@H]2O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]3[C@H]([C@H]([C@@H](O3)N4C=CC(=O)NC4=O)O)O)O
FormulaC22 H33 N4 O20 P3
Name(2R,3R,4S,5S)-3,4-dihydroxy-5-[({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methyl)amino]tetrahydro-2H-pyr an-2-yl [(2R,3S,4R,5R)-5-(2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl dihydrogen diphosphate;
PLP-UDP-Ara4N
ChEMBL
DrugBank
ZINCZINC000098208240
PDB chain4oca Chain A Residue 400 [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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PDB4oca Structural Basis for Substrate Specificity in ArnB. A Key Enzyme in the Polymyxin Resistance Pathway of Gram-Negative Bacteria.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		F13 S14 P16 A63 T64 W89 D160 A162 H163 S183 H185 A186 I187 H329 F330
Binding residue
(residue number reindexed from 1)		F6 S7 P9 A56 T57 W82 D153 A155 H156 S176 H178 A179 I180 H308 F309
Annotation score1
Gene Ontology
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UnboundLocalError		Python 3.6.8: /usr/bin/python3
Fri Nov 15 09:44:53 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 = '4oca', asym_id = 'A', bs = 'BS01', title = 'Structural Basis for Substrate Specificity in Ar...xin Resistance Pathway of Gram-Negative Bacteria.'
 /var/www/html/BioLiP/pdb.cgi in display_interaction(pdbid='4oca', asym_id='A', bs='BS01', title='Structural Basis for Substrate Specificity in Ar...xin Resistance Pathway of Gram-Negative Bacteria.')
   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 = '0008483', uniprot = '', pdbid = '4oca', asym_id = 'A'
 /var/www/html/BioLiP/pdb.cgi in display_go(go='0008483', uniprot='', pdbid='4oca', asym_id='A')
    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>