KpKP13 Protein target profile

LpxA-like domain-containing transferase

Accession: KP13_00363

Gene: AHE46898.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKW1
Length 151
Pocket druggability (P2Rank · AlphaFold DB model) 0.049
Direct ligand evidence 0 66 total records
Functional annotation 0 EC 0 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing 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
1.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
50.0 Higher values support similarity to known essential genes.
DEG E-value
0.4 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.54 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.049
Structure A0A0H3GKW1
Pocket Pocket 1
Druggability (FPocket) 0.258
Structure A0A0H3GKW1
Pocket Pocket 1
ColabFold model
P2Rank 0.039 · Pocket 1
FPocket 0.17 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 56 / 4744 genomes with a hit
Prevalence 1.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MPELRDTGVRNVVCGENVVIYQPANLYDCQLGDNVFVGPFVEIQGNTRIGANSKIQSHTFICEYVTIGQRCFIGHGVMFANDLFREGKPNADRASWGRIEIGDDVSIGSGATILAVSICDGVVIGAGSVVTKSITEKGVWAGNPARLLRRL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

Subcellular localization

Localization
Unknown

No GO or EC annotations are currently loaded for this protein.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
5 150 Gene3D G3DSA:2.160.10.10 Hexapeptide repeat proteins
15 149 PANTHER PTHR43300 ACETYLTRANSFERASE
65 74 Pfam PF14602 Hexapeptide repeat of succinyl-transferase
65 74 InterPro IPR001451 Hexapeptide repeat
99 132 Pfam PF14602 Hexapeptide repeat of succinyl-transferase
99 132 InterPro IPR001451 Hexapeptide repeat
11 151 SUPERFAMILY SSF51161 Trimeric LpxA-like enzymes
11 151 InterPro IPR011004 Trimeric LpxA-like superfamily
31 149 CDD cd03358 LbH_WxcM_N_like
28 61 Pfam PF00132 Bacterial transferase hexapeptide (six repeats)
28 61 InterPro IPR001451 Hexapeptide repeat

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.

Download VMD script Full viewer

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Drag to rotate — click the view, then scroll to zoom.

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.049
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.258
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

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
AlphaFold DB AF_A0A0H3GKW1
AlphaFold DB full sequence Viewing
ColabFold KP13_00363
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.

66 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 16 records from similar proteins
Structural ligands 16 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1F7 PDB via homolog 584.7 Da · LogP 3.04 · TPSA 182.5 Open detail RCSB PDB
4TG PDB via homolog Detail RCSB PDB
FTT PDB via homolog Detail RCSB PDB
O3V PDB via homolog Detail RCSB PDB
O3Y PDB via homolog Detail RCSB PDB

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
1F7 RCSB PDB P21645 584.7 Da LogP 3.04 TPSA 182.5 2 viol. ✓ Clean CCCCCCCCCCC[C@H](CC(=O)SCCNC(=O)CCNC(=O)[C@H](C…
4TG RCSB PDB Q12KT8 575.4 Da LogP -2.67 TPSA 265.4 3 viol. ✓ Clean C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OP(=O)(O)OP…
FTT RCSB PDB P21645 244.4 Da LogP 3.74 TPSA 57.5 ✓ Ro5 ✓ Clean CCCCCCCCCCC[C@H](CC(=O)O)O
O3V RCSB PDB P21645 389.5 Da LogP 5.01 TPSA 68.0 1 viol. ✓ Clean CC1(Cc2c(c(c3c(n2)nn(c3O)c4ccccc4)c5cccs5)C(=O)…
O3Y RCSB PDB P21645 417.9 Da LogP 5.60 TPSA 68.0 1 viol. ✓ Clean CC1(Cc2c(c(c3c(n2)nn(c3O)c4ccccc4)c5ccccc5Cl)C(…
O4D RCSB PDB P21645 396.5 Da LogP 1.68 TPSA 77.2 ✓ Ro5 ✓ Clean Cc1cc(nc2c1c(nn2CC(=O)NCCCN3CCOCC3)n4cccc4)C
O4G RCSB PDB P21645 364.4 Da LogP 3.56 TPSA 89.8 ✓ Ro5 ✓ Clean c1cc(cc(c1)NC(=O)c2ccco2)NC(=O)c3ccc4c(c3)OCCO4
O4P RCSB PDB P21645 406.5 Da LogP 4.86 TPSA 54.6 ✓ Ro5 ✓ Clean CN([C@@H](c1cccs1)c2c[nH]c3c2cccc3)C(=O)COc4ccc…
O4S RCSB PDB P21645 474.6 Da LogP 3.51 TPSA 73.0 ✓ Ro5 ✓ Clean CCc1ccc(cc1)CNC(=O)CN2c3cc(ccc3N4CCCC[C@@H]4C2=…
O4V RCSB PDB P21645 358.4 Da LogP 2.39 TPSA 100.1 ✓ Ro5 ✓ Clean CCOc1ccccc1n2c(c(nn2)S(=O)(=O)c3ccc(cc3)C)N
PNS RCSB PDB P21645 358.4 Da LogP -0.96 TPSA 145.2 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
SXA RCSB PDB P26839 400.4 Da LogP -0.61 TPSA 162.3 ✓ Ro5 ✓ Clean CC(=O)SCCNC(=O)CCNC(=O)[C@H](C(C)(C)COP(=O)(O)O…
T3F RCSB PDB Q6TFC6 547.3 Da LogP -2.46 TPSA 262.3 3 viol. ✓ Clean C[C@@H]1[C@@H]([C@@H]([C@H]([C@H](O1)O[P@@](=O)…
T3Q RCSB PDB Q6TFC6 547.3 Da LogP -2.46 TPSA 262.3 3 viol. ✓ Clean C[C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[P@](=O)(O…
TDR RCSB PDB Q12KT8 126.1 Da LogP -0.63 TPSA 65.7 ✓ Ro5 ✓ Clean CC1=CNC(=O)NC1=O
TYD RCSB PDB Q12KT8 402.2 Da LogP -1.28 TPSA 197.6 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…

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.