Protein target profile

KP13_00092

2-aminoethylphosphonate--pyruvate transaminase

Genome: KpKP13 Gene: phnW AHE42017.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GYY8
Length 367
Pocket druggability 0.379
Direct ligand evidence 0 77 total records
Functional annotation 1 EC 3 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
Hit
Human identity (%)
25.625 Lower values reduce human off-target concern.
Human E-value
1.2e-20
Gut microbiome similarity
8.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.3 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.379
Structure A0A0H3GYY8
Pocket Pocket 1
P2Rank 0.334
Structure A0A0H3GYY8
Pocket Pocket 1
ColabFold model
FPocket 0.218 · Pocket 2
P2Rank 0.44 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 389 / 4744 genomes with a hit
Prevalence 8.2%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTSRNYLLLTPGPLTTSRTVKEAMLFDSCTWDDDYNLGVVQTIRQQLVQLATPADGYTAVLLQGSGSYAVEAVLGSVIGEQGKVLIVSNGAYGARMIEMAQLMGIACHPYDCGEVSRPDAAAIEQILQNDPAITHIAMVHSETTTGMLNPIAEVAELAKRYDKRYIVDAMSSFGGIPLDIAALNIDYLISSANKCIQGVPGFAFVIAREAELAACKGRSRSLSLDLYAQWRCMEDNHGKWRFTSPTHTVLAFAQALKELAQEGGVSARHQRYRNNQRRLVAGMRALGFRPLLDDSLHSPIITAFYSPDAPQYRFHTFYQKLKDQGFVIYPGKVSQSDCFRIGNIGEVYDADITALLAAIDNAMYWKQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0019700 The chemical reactions and pathways resulting in the breakdown of phosphonates, any organic compound containing one or more C-PO(OH)2 or C-PO(OR)2 (with R=alkyl, aryl) groups. Catabolism of phosphonic acid itself, an inorganic compound without the biochemically relevant C-P bond, is not included.
  • GO:0047304 Catalysis of the reaction: (2-aminoethyl)phosphonate + pyruvate = L-alanine + phosphonoacetaldehyde.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
1 367 Hamap MF_01376 2-aminoethylphosphonate--pyruvate transaminase [phnW].
1 367 InterPro IPR012703 2-aminoethylphosphonate--pyruvate transaminase
9 354 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
9 354 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
40 302 Pfam PF00266 Aminotransferase class-V
40 302 InterPro IPR000192 Aminotransferase class V domain
4 366 NCBIfam TIGR02326 2-aminoethylphosphonate--pyruvate transaminase
4 366 InterPro IPR012703 2-aminoethylphosphonate--pyruvate transaminase
17 262 Gene3D G3DSA:3.40.640.10 -
17 262 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
1 365 PIRSF PIRSF000524 SPT
1 365 InterPro IPR024169 Serine-pyruvate aminotransferase/2-aminoethylphosphonate-pyruvate transaminase
2 366 PANTHER PTHR42778 2-AMINOETHYLPHOSPHONATE--PYRUVATE TRANSAMINASE
7 363 NCBIfam TIGR03301 2-aminoethylphosphonate aminotransferase
7 363 InterPro IPR012703 2-aminoethylphosphonate--pyruvate transaminase
6 363 SUPERFAMILY SSF53383 PLP-dependent transferases
6 363 InterPro IPR015424 Pyridoxal phosphate-dependent transferase

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

Loading 3D structure...

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 · FPocket

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

Site 1 FPocket #1
0.379
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.334
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.024
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.008
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.004
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:340-340
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_A0A0H3GYY8
AlphaFold DB full sequence Viewing
ColabFold KP13_00092
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.

77 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 27 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 20 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AOA PDB via homolog 91.1 Da · LogP -1.04 · TPSA 72.5 Open detail RCSB PDB
BTB PDB via homolog Detail RCSB PDB
KY1 PDB via homolog Detail RCSB PDB
MMM PDB via homolog Detail RCSB PDB
PLR 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
AOA RCSB PDB P21549 91.1 Da LogP -1.04 TPSA 72.5 ✓ Ro5 ✓ Clean C(C(=O)O)ON
BTB RCSB PDB P21549 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
KY1 RCSB PDB Q7PRG3 193.2 Da LogP 1.32 TPSA 80.4 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)CCC(=O)O)N
MMM RCSB PDB Q5SLX0 348.2 Da LogP -0.04 TPSA 169.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\[C@@](C)(CO)C(=O)…
PLR RCSB PDB P21549 233.2 Da LogP 1.01 TPSA 99.9 ✓ Ro5 ✓ Clean Cc1c(cnc(c1O)C)COP(=O)(O)O
PMP RCSB PDB P21549 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
POA RCSB PDB P96060 124.0 Da LogP -0.64 TPSA 74.6 ✓ Ro5 ✓ Clean C(C=O)P(=O)(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.