Protein target profile

KP13_03591

UDP-2,3-diacylglucosamine hydrolase

Genome: KpKP13 Gene: lpxH AHE45934.1 3D evidence: Experimental + ColabFold model UniProt A6T5R0
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Length 240
Pocket druggability 0.994
Direct ligand evidence 2 52 total records
Functional annotation 0 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.99, P2Rank 0.94). Use the 3D pocket comparison to verify whether they identify the same site. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Direct ligand evidence 2 direct ligand records. Strong known ligand: co-crystal structure 2 PDB record(s) show a ligand actually co-crystallized with this exact protein - real experimental evidence, not a computational prediction. Review the complete evidence below

Risks to review

Microbiome similarity 141 of 4744 screened genomes (3.0%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.99) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
83.75 Higher values support similarity to known essential genes.
DEG E-value
3.88e-152 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.81 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.994
Structure 6PH9
Pocket Pocket 1
P2Rank 0.941
Structure 6PH9
Pocket Pocket 1
ColabFold model
FPocket 0.952 · Pocket 14
P2Rank 0.956 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 141 / 4744 genomes with a hit
Prevalence 3.0%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A6T5R0

Structure

PDB 6PH9 PDB 6PIB PDB 6PJ3 PDB 6WII PDB 7SS6 PDB 7SS7 PDB 8QK2 PDB 8QK5 PDB 8QKA PDB 9CCX PDB 9CCY PDB 9CCZ PDB 9CD0 PDB 9CD1 PDB 9ENG

Sequence

Primary amino-acid sequence viewer.

MATLFIADLHLQTEEPAITAGFLRFLQGEARQADALYILGDLFEAWIGDDDPNPLHQQIASAIKAVVDAGVPCYFIHGNRDFLVGERFARQSGMILLAEEERLDLYGREVLIMHGDTLCTDDQGYLAFRAKVHTPWIQRLFLALPLFIRRRIAARMRADSKAANSSKSMEIMDVNPQAVVDAMERHHVQWLIHGHTHRPAVHELQANGQPAWRVVLGAWHSEGSMVKVTPDDVELIHFPF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0016462 Catalysis of the hydrolysis of a pyrophosphate bond (diphosphate bond) between two phosphate groups.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
1 209 Gene3D G3DSA:3.60.21.10 -
1 209 InterPro IPR029052 Metallo-dependent phosphatase-like
2 238 PANTHER PTHR34990 UDP-2,3-DIACYLGLUCOSAMINE HYDROLASE-RELATED
2 238 InterPro IPR043461 UDP-2,3-diacylglucosamine hydrolase LpxH-like
3 232 NCBIfam TIGR01854 UDP-2,3-diacylglucosamine diphosphatase
3 232 InterPro IPR010138 UDP-2,3-diacylglucosamine hydrolase
3 199 Pfam PF00149 Calcineurin-like phosphoesterase
3 199 InterPro IPR004843 Calcineurin-like phosphoesterase domain, ApaH type
1 240 Hamap MF_00575 UDP-2,3-diacylglucosamine hydrolase [lpxH].
1 240 InterPro IPR010138 UDP-2,3-diacylglucosamine hydrolase
1 224 SUPERFAMILY SSF56300 Metallo-dependent phosphatases
1 224 InterPro IPR029052 Metallo-dependent phosphatase-like
4 219 CDD cd07398 MPP_YbbF-LpxH
1 140 FunFam G3DSA:3.60.21.10:FF:000012 UDP-2,3-diacylglucosamine hydrolase

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.994
Likely same site as P2Rank 1 4.1 Å 28 shared residues 90% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.941
Likely same site as FPocket 1 4.1 Å 28 shared residues 90% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.406
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.03
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.012
Show in viewer
Surrounding area
All structural evidence 15 experimental · 1 predicted

Structural evidence

15 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 6PH9
X-ray — A —
PDBe RCSB PDBj File
Viewing
PDB 6PIB
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 6PJ3
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 6WII
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 7SS6
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 7SS7
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 8QK2
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 8QK5
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 8QKA
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 9CCX
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 9CCY
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 9CCZ
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 9CD0
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 9CD1
X-ray — A —
PDBe RCSB PDBj File
Loaded
PDB 9ENG
X-ray — A —
PDBe RCSB PDBj File
Loaded
ColabFold KP13_03591
ColabFold — — full sequence — Loaded

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 2 same-protein records
Transferred evidence 0 records from similar proteins
Structural ligands 2 2 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
LP5 PDB co-crystal 711.9 Da · LogP 4.91 · TPSA 212.3 Open detail RCSB PDB
OKV PDB co-crystal Detail RCSB PDB
ZINC20181932 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1857791959 ZINC proposed compound · Tanimoto 0.780 Detail ZINC
ZINC1857791964 ZINC proposed compound · Tanimoto 0.780 Detail ZINC

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

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
LP5 RCSB PDB
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 RCSB PDB
6PIB Open crystal
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.