Structure of PDB 8qjz Chain A Binding Site BS03

Receptor Information
>8qjz Chain A (length=239) Species: 562 (Escherichia coli) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ATLFIADLHLCVEEPAITAGFLRFLAEEARKADALYILGDLFEAWIGDDD
PNPLHRQMAAAIKAVSDSGVPCYFIHGNRDFLLGKRFARESGMTLLPEEK
VLELYGRRVLIMHGDTLCTDDAGYQAFRAKVHKPWLQMLFLALPLFVRKR
IAARMRANSKEANSSKSLAIMDVNQNAVVSAMEKHQVQWLIHGHTHRPAV
HELIANQQPAFRVVLGAWHTEGSMVKVTADDVELIHFPF
Ligand information
Ligand IDLP5
InChIInChI=1S/C34H66NO12P/c1-3-5-7-9-11-13-15-17-19-21-26(37)23-29(39)35-31-33(32(41)28(25-36)45-34(31)47-48(42,43)44)46-30(40)24-27(38)22-20-18-16-14-12-10-8-6-4-2/h26-28,31-34,36-38,41H,3-25H2,1-2H3,(H,35,39)(H2,42,43,44)/t26-,27-,28-,31-,32-,33-,34-/m1/s1
InChIKeyHEHQDWUWJVPREQ-XQJZMFRCSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCCCCCCCCC[C@@H](O)CC(=O)N[C@H]1[C@H](O[C@H](CO)[C@@H](O)[C@@H]1OC(=O)C[C@H](O)CCCCCCCCCCC)O[P](O)(O)=O
OpenEye OEToolkits 1.5.0CCCCCCCCCCC[C@H](CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)O)CO)O)OC(=O)C[C@@H](CCCCCCCCCCC)O)O
ACDLabs 10.04O=P(OC1OC(C(O)C(OC(=O)CC(O)CCCCCCCCCCC)C1NC(=O)CC(O)CCCCCCCCCCC)CO)(O)O
OpenEye OEToolkits 1.5.0CCCCCCCCCCCC(CC(=O)NC1C(C(C(OC1OP(=O)(O)O)CO)O)OC(=O)CC(CCCCCCCCCCC)O)O
CACTVS 3.341CCCCCCCCCCC[CH](O)CC(=O)N[CH]1[CH](O[CH](CO)[CH](O)[CH]1OC(=O)C[CH](O)CCCCCCCCCCC)O[P](O)(O)=O
FormulaC34 H66 N O12 P
Name(R)-((2R,3S,4R,5R,6R)-3-HYDROXY-2-(HYDROXYMETHYL)-5-((R)-3-HYDROXYTETRADECANAMIDO)-6-(PHOSPHONOOXY)TETRAHYDRO-2H-PYRAN-4-YL) 3-HYDROXYTETRADECANOATE
ChEMBL
DrugBank
ZINCZINC000058650130
PDB chain8qjz Chain A Residue 303 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB8qjz Antibiotic class with potent in vivo activity targeting lipopolysaccharide synthesis in Gram-negative bacteria.
Resolution1.35 Å
Binding residue
(original residue number in PDB)		N79 R80 L83 Y125 L137 F141 M156 R157 N159 S160 N164 K167 H195
Binding residue
(residue number reindexed from 1)		N78 R79 L82 Y124 L136 F140 M155 R156 N158 S159 N163 K166 H194
Annotation score4
Enzymatic activity
Enzyme Commision number 3.6.1.54: UDP-2,3-diacylglucosamine diphosphatase.
Gene Ontology
Molecular Function
GO:0008758 UDP-2,3-diacylglucosamine hydrolase activity
GO:0016462 pyrophosphatase activity
GO:0016787 hydrolase activity
GO:0030145 manganese ion binding
GO:0046872 metal ion binding
Biological Process
GO:0009245 lipid A biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005886 plasma membrane
GO:0019897 extrinsic component of plasma membrane

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Molecular Function
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Biological Process
View graph for
Cellular Component
External links
PDB RCSB:8qjz, PDBe:8qjz, PDBj:8qjz
PDBsum8qjz
PubMed38579010
UniProtA0A066QL39

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