Protein profile

PA3646

UDP-3-O-acylglucosamine N-acyltransferase

Genome: NC_002516.2

Gene: lpxD PA3646 Structure source: Experimental + AlphaFold UniProt Q9HXY6
Export view
Amino acids 353
Annotations 8
Features 20
PDB binders 27
Druggability 0.649

Overview

Basic information about this protein and its source genome.

Accession
PA3646
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
lpxD PA3646
Status
annotated
Amino acids
353
Structure source
Experimental + AlphaFold
EC
2.3.1.191
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0016410 Catalysis of the transfer of an acyl group to a nitrogen atom on the acceptor molecule. GO:0103118 Catalysis of the reaction: a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + a (3R)-hydroxyacyl-[ACP] = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + holo-[ACP] + H+. GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common. GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.649
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MMSTLSYTLGQLAAHVGAEVRGDADLPIQGLATLQEAGPAQLSFLANPQYRKYLPESRAGAVLLTAADADGFAGTALVVANPYLAYASLSHLFDRKPKAAAGIHPTAIVAADAEVDPSASVGAYAVIESGARIGAGVSIGAHCVIGARSVIGEGGWLAPRVTLYHDVTIGARVSIQSGAVIGGEGFGFANEKGVWQKIAQIGGVTIGDDVEIGANTTIDRGALSDTLIGNGVKLDNQIMIAHNVQIGDHTAMAACVGISGSAKIGRHCMLAGGVGLVGHIEICDNVFVTGMTMVTRSITEPGSYSSGTAMQPAAEWKKSAARIRQLDDMARRLQQLEKRLAAVTSSGDASSDA

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0016410 Catalysis of the transfer of an acyl group to a nitrogen atom on the acceptor molecule.
  • GO:0103118 Catalysis of the reaction: a UDP-3-O-[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + a (3R)-hydroxyacyl-[ACP] = a UDP-2-N,3-O-bis[(3R)-3-hydroxyacyl]-alpha-D-glucosamine + holo-[ACP] + H+.
  • GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • GO:0016747 Catalysis of the transfer of an acyl group, other than amino-acyl, from one compound (donor) to another (acceptor).

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
319 346 Coils Coil Coil
12 329 Hamap MF_00523 UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase [lpxD].
12 329 InterPro IPR007691 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD
149 183 Pfam PF00132 Bacterial transferase hexapeptide (six repeats)
149 183 InterPro IPR001451 Hexapeptide repeat
11 332 NCBIfam TIGR01853 UDP-3-O-(3-hydroxymyristoyl)glucosamine N-acyltransferase
11 332 InterPro IPR007691 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD
2 101 Gene3D G3DSA:3.40.1390.10 -
313 353 Gene3D G3DSA:1.20.5.170 -
7 340 PANTHER PTHR43378 UDP-3-O-ACYLGLUCOSAMINE N-ACYLTRANSFERASE
7 340 InterPro IPR007691 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD
109 137 ProSitePatterns PS00101 Hexapeptide-repeat containing-transferases signature.
109 137 InterPro IPR018357 Hexapeptide transferase, conserved site
112 317 CDD cd03352 LbH_LpxD
112 317 InterPro IPR007691 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase LpxD
102 312 Gene3D G3DSA:2.160.10.10 Hexapeptide repeat proteins
25 92 Pfam PF04613 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, LpxD
25 92 InterPro IPR020573 UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase, non-repeat region
35 320 SUPERFAMILY SSF51161 Trimeric LpxA-like enzymes
35 320 InterPro IPR011004 Trimeric LpxA-like superfamily

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

Loading 3D structure...

Legend High Medium Low

Structural evidence

3 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 3PMO
X-ray 1.30 Å A
99.7% 2-353
PDBe RCSB PDBj File
Viewing
PDB 6UED
X-ray 1.55 Å A
99.4% 3-353
PDBe RCSB PDBj File
Loaded
PDB 6UEC
X-ray 2.60 Å A
99.2% 3-352
PDBe RCSB PDBj File
Loaded
AlphaFold PA3646
AlphaFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
4 0.649
2 0.521
1 0.408
5 0.263

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 6.68 0.339
2 4.26 0.175
3 2.07 0.046
4 1.61 0.025
5 0.94 0.004

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

77 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
Q5M
6UEC 2.60 Å Open crystal
228.2 Da LogP 2.89 TPSA 54.4 ✓ Ro5 ✓ Clean c1ccc2c(c1)cccc2C(=O)CCC(=O)O

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.