Structure of PDB 8v24 Chain D Binding Site BS01

Receptor Information
>8v24 Chain D (length=302) Species: 199310 (Escherichia coli CFT073) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MIKQRTLKRIVQATGVGLHTGKKVTLTLRPAPANTGVIYRRTDLNPPVDF
PADAKSVRDTMLCTCLVNEHDVRISTVEHLNAALAGLGIDNIVIEVNAPE
IPIMDGSAAPFVYLLLDAGIDELNCAKKFVRIKETVRVEDGDKWAEFKPY
NGFSLDFTIDFNHPAIDSSNQRYAMNFSADAFMRQISRARTFGFMRDIEY
LQSRGLCLGGSFDCAIVVDDYRVLNEDGLRFEDEFVRHKMLDAIGDLFMC
GHNIIGAFTAYKSGHALNNKLLQAVLAKQEAWEYVTFQDDAELPLAFKAP
SA
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 chain8v24 Chain D Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB8v24 Dual function of LapB (YciM) in regulating Escherichia coli lipopolysaccharide synthesis.
Resolution3.6 Å
Binding residue
(original residue number in PDB)
L62 F161 F192 F194 I198 C207 G210 S211 A215 V217 K239 K262
Binding residue
(residue number reindexed from 1)
L62 F161 F192 F194 I198 C207 G210 S211 A215 V217 K239 K262
Annotation score1
Enzymatic activity
Enzyme Commision number 3.5.1.108: UDP-3-O-acyl-N-acetylglucosamine deacetylase.
Gene Ontology
Molecular Function
GO:0016787 hydrolase activity
GO:0046872 metal ion binding
GO:0103117 UDP-3-O-acyl-N-acetylglucosamine deacetylase activity
Biological Process
GO:0006796 phosphate-containing compound metabolic process
GO:0009245 lipid A biosynthetic process
GO:0019637 organophosphate metabolic process
GO:1901135 carbohydrate derivative metabolic process

View graph for
Molecular Function

View graph for
Biological Process
External links
PDB RCSB:8v24, PDBe:8v24, PDBj:8v24
PDBsum8v24
PubMed38635633
UniProtP0A726|LPXC_ECOL6 UDP-3-O-acyl-N-acetylglucosamine deacetylase (Gene Name=lpxC)

[Back to BioLiP]