Protein profile

VK055_2067

UDP-2,3-diacylglucosamine hydrolase

Genome: KpATCC43816

Gene: lpxH AIK80672.1 Structure source: Experimental + ColabFold UniProt A6T5R0
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Amino acids 232
Annotations 4
Features 13
PDB binders 2
Druggability 0.994

Overview

Basic information about this protein and its source genome.

Accession
VK055_2067
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
lpxH AIK80672.1
Status
annotated
Amino acids
232
Structure source
Experimental + ColabFold
GO
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:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0016462 Catalysis of the hydrolysis of a pyrophosphate bond (diphosphate bond) between two phosphate groups.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
82.759
DEG E-value
4.61e-146
Localization
Cytoplasmic
ColabFold pLDDT
96.51

Selected Druggability evidence

PDB experimental structure

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 0.994
Structure 6PH9
Pocket Pocket 1
P2Rank 0.941
Structure 6PH9
Pocket Pocket 1
ColabFold model
FPocket 0.906 · Pocket 7
P2Rank 0.944 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 125 / 4744 genomes with a hit
Normalized 0.026

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • 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:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016462 Catalysis of the hydrolysis of a pyrophosphate bond (diphosphate bond) between two phosphate groups.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
1 211 CDD cd07398 MPP_YbbF-LpxH
1 201 Gene3D G3DSA:3.60.21.10 -
1 201 InterPro IPR029052 Metallo-dependent phosphatase-like
1 224 NCBIfam TIGR01854 UDP-2,3-diacylglucosamine diphosphatase
1 224 InterPro IPR010138 UDP-2,3-diacylglucosamine hydrolase
1 232 Hamap MF_00575 UDP-2,3-diacylglucosamine hydrolase [lpxH].
1 232 InterPro IPR010138 UDP-2,3-diacylglucosamine hydrolase
2 216 SUPERFAMILY SSF56300 Metallo-dependent phosphatases
2 216 InterPro IPR029052 Metallo-dependent phosphatase-like
16 191 Pfam PF00149 Calcineurin-like phosphoesterase
16 191 InterPro IPR004843 Calcineurin-like phosphoesterase domain, ApaH type
1 230 PANTHER PTHR34990 UDP-2,3-DIACYLGLUCOSAMINE HYDROLASE-RELATED
1 230 InterPro IPR043461 UDP-2,3-diacylglucosamine hydrolase LpxH-like

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

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Structural evidence

1 + 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 6PH9
X-ray 20.00 Å - —
PDBe RCSB PDBj File
Viewing
ColabFold VK055_2067
ColabFold — — 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
1 0.994

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 31.91 0.941
2 7.68 0.406
3 1.71 0.03
4 1.26 0.012

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.

52 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
LP5
6PH9 Open crystal
711.9 Da LogP 4.91 TPSA 212.3 2 viol. ✓ Clean CCCCCCCCCCC[C@H](CC(=O)N[C@@H]1[C@H]([C@@H]([C@…
OKV
6PIB
453.5 Da LogP 3.13 TPSA 60.9 ✓ Ro5 ✓ Clean CC(=O)N1CCc2c1ccc(c2)S(=O)(=O)N3CCN(CC3)c4cccc(…

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.