Structure of PDB 8gjh Chain B Binding Site BS01

Receptor Information
>8gjh Chain B (length=638) 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]
MKAVIFAYHDMGCQGVQAVLDAGYEIAAIFTHADGSVSRQAAELGIPVYA
PDNVNHPIWVDRIAELAPDIIFSFYYRNLLSEEILHLAPAGAFNLHGSLL
PAYRGRAPLNWVLVNGESETGVTLHRMVKRADAGEIVASQRVAIAQDDVA
LTLHHKLCQAARQLLNSILPTMKCGDIPSVPQRESDSTYYGRRRPEDGLI
DWHKPVSTVHNLVRAVAAPWPGAFSYNGSQKFTIWSSRMCPDAQGALPGS
VISVSPLRVACADGALEIITGQAGDDITVQGSQLAQTLGLVAGARLRRIR
VLILGVNGFIGNHLTERLLNEENYEVYGMDIGSNAISRFLLHPRFHFVEG
DISIHSEWIEYHVKKCDVVLPLVAIATPIEYTRNPLRVFELDFEENLRII
RYCVKYRKRVVFPSTSEVYGMCTDASFDEDKSNLIVGPVNKPRWIYSVSK
QLLDRVIWAYGEKEGLRFTLFRPFNWMGPRLDSLNAARIGSSRAITQLIL
NLVEGTPIKLIDGGQQKRCFTDIRDGIEALFRIIVNDGDRCDGKIINIGN
PDNEASIQELATLLLDSFDKHPLRCHFPPFAGFQVVESRSYYGKGYQDVA
HRKPSIDNARRCLGWEPSIAMRDTVEETLDFFLRSVDI
Ligand information
Ligand IDUGA
InChIInChI=1S/C15H22N2O18P2/c18-5-1-2-17(15(26)16-5)12-9(22)6(19)4(32-12)3-31-36(27,28)35-37(29,30)34-14-10(23)7(20)8(21)11(33-14)13(24)25/h1-2,4,6-12,14,19-23H,3H2,(H,24,25)(H,27,28)(H,29,30)(H,16,18,26)/t4-,6-,7+,8+,9-,10-,11+,12-,14-/m1/s1
InChIKeyHDYANYHVCAPMJV-LXQIFKJMSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C(O)C3OC(OP(=O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O)C(O)C(O)C3O
CACTVS 3.341O[CH]1[CH](O)[CH](O[CH]([CH]1O)C(O)=O)O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)O[P@@](=O)(O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)C(=O)O)O)O)O)O)O
CACTVS 3.341O[C@@H]1[C@@H](O)[C@H](O[C@@H]([C@H]1O)C(O)=O)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
OpenEye OEToolkits 1.5.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)OC3C(C(C(C(O3)C(=O)O)O)O)O)O)O
FormulaC15 H22 N2 O18 P2
NameURIDINE-5'-DIPHOSPHATE-GLUCURONIC ACID;
UDP-GLUCURONIC ACID
ChEMBLCHEMBL228057
DrugBankDB03041
ZINCZINC000008215691
PDB chain8gjh Chain B Residue 1100 [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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PDB8gjh Targeting the Conformational Change in ArnA Dehydrogenase for Selective Inhibition of Polymyxin Resistance.
Resolution3.6 Å
Binding residue
(original residue number in PDB)		A393 Y398 T432 S433 E434 R460 N492 R510 A511 K526 L527 I528 Q533 R535 I574 Y609 D615 R619
Binding residue
(residue number reindexed from 1)		A376 Y381 T415 S416 E417 R443 N475 R493 A494 K509 L510 I511 Q516 R518 I557 Y592 D598 R602
Annotation score4
Enzymatic activity
Enzyme Commision number 1.1.1.305: UDP-glucuronic acid oxidase (UDP-4-keto-hexauronic acid decarboxylating).
2.1.2.13: UDP-4-amino-4-deoxy-L-arabinose formyltransferase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0016491 oxidoreductase activity
GO:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor
GO:0016740 transferase activity
GO:0016742 hydroxymethyl-, formyl- and related transferase activity
GO:0016831 carboxy-lyase activity
GO:0099618 UDP-glucuronic acid dehydrogenase activity
GO:0099619 UDP-4-amino-4-deoxy-L-arabinose formyltransferase activity
Biological Process
GO:0009058 biosynthetic process
GO:0009103 lipopolysaccharide biosynthetic process
GO:0009245 lipid A biosynthetic process
GO:0046493 lipid A metabolic process
GO:0046677 response to antibiotic

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:8gjh, PDBe:8gjh, PDBj:8gjh
PDBsum8gjh
PubMed37410993
UniProtO52325|ARNA_SALTY Bifunctional polymyxin resistance protein ArnA (Gene Name=arnA)

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