Protein target profile

KP13_02854

Putrescine aminotransferase

Genome: KpKP13 Gene: patA AHE42577.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GXV4
Length 459
Pocket druggability 0.485
Direct ligand evidence 0 67 total records
Functional annotation 2 EC 8 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 (%)
33.333 Lower values reduce human off-target concern.
Human E-value
2.25e-61
Gut microbiome similarity
1.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.87 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 0.485
Structure A0A0H3GXV4
Pocket Pocket 6
P2Rank 0.651
Structure A0A0H3GXV4
Pocket Pocket 1
ColabFold model
FPocket 0.378 · Pocket 4
P2Rank 0.421 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 77 / 4744 genomes with a hit
Prevalence 1.6%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MNRLPSSASALACSAHALNLIEKRTLDHEEMKALNQEVREYFKEHVNPGFLEYRKSVTAGGDYGAVEWQAGGLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVENQLAKQPLHSQELLDPLRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSATAKSTFRKPFMPLLPGFRHVPFGDITAMRTMLSECKKTGDDVAAVILEPIQGEGGVILPPTGYLPAVRKLCDEFGALLILDEVQTGMGRTGKMFACEHENVQPDILCLAKALGGGVMPIGATVATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLTQNLPAQAAQKGDMLLDGFRLLAQEYPDLVNEVRGKGMLMAIEFVDNEIGYDFASEMFRQRVLVAGTLNNAKTIRIEPPLTLTLEQCEQVLKAARKALAALRVSVEEA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 8 GO

Enzyme Commission (EC)

2

Gene Ontology (GO)

8
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
  • GO:0009447 The chemical reactions and pathways resulting in the breakdown of putrescine, 1,4-diaminobutane; putrescine is the metabolic precursor of spermidine and spermine.
  • 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:0033094 Catalysis of the reaction: putrescine + 2-oxoglutarate = L-glutamate + 1-pyrroline + H2O. The enzymatic part of the reaction produces 4-aminobutanal that spontaneously cyclizes to form 1-pyrroline.
  • GO:0019161 Catalysis of the reaction: an alpha,omega-diamine + 2-oxoglutarate = an omega-aminoaldehyde + L-glutamate.
  • GO:0042802 Binding to an identical protein or proteins.
  • GO:0019477 The chemical reactions and pathways resulting in the breakdown of L-lysine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
4 12 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
35 447 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
35 447 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
1 459 Hamap MF_01276 Putrescine aminotransferase [patA].
1 459 InterPro IPR017747 Putrescine aminotransferase
18 459 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
74 449 Pfam PF00202 Aminotransferase class-III
74 449 InterPro IPR005814 Aminotransferase class-III
100 353 FunFam G3DSA:3.40.640.10:FF:000004 Acetylornithine aminotransferase
13 17 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
8 449 NCBIfam TIGR03372 putrescine aminotransferase
8 449 InterPro IPR017747 Putrescine aminotransferase
435 455 Coils Coil Coil
74 450 SUPERFAMILY SSF53383 PLP-dependent transferases
74 450 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
100 353 Gene3D G3DSA:3.40.640.10 -
100 353 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
268 305 ProSitePatterns PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.
268 305 InterPro IPR005814 Aminotransferase class-III
62 451 PANTHER PTHR11986 AMINOTRANSFERASE CLASS III
52 209 PIRSF PIRSF000521 Transaminase_4ab_Lys_Orn
52 209 InterPro IPR005814 Aminotransferase class-III
213 452 PIRSF PIRSF000521 Transaminase_4ab_Lys_Orn
213 452 InterPro IPR005814 Aminotransferase class-III
74 440 CDD cd00610 OAT_like
74 440 InterPro IPR005814 Aminotransferase class-III
1 17 Phobius SIGNAL_PEPTIDE Signal peptide region

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 #6
0.485
Likely same site as P2Rank 2 1.1 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #4
0.332
Likely same site as P2Rank 4 2.2 Å 9 shared residues 100% of smaller site
Unusual size
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Surrounding area
Site 3 FPocket #7
0.329
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Surrounding area
Site 4 FPocket #11
0.244
Likely same site as P2Rank 1 7.7 Å 8 shared residues 89% of smaller site
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.651
Likely same site as FPocket 11 7.7 Å 8 shared residues 89% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.41
Likely same site as FPocket 6 1.1 Å 12 shared residues 100% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.31
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Surrounding area
Site 4 P2Rank #4
0.152
Likely same site as FPocket 4 2.2 Å 9 shared residues 100% of smaller site
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Surrounding area
Site 5 P2Rank #5
0.059
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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_A0A0H3GXV4
AlphaFold DB full sequence Viewing
ColabFold KP13_02854
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.

67 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 17 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 4 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
9QJ PDB via homolog 358.3 Da · LogP 1.38 · TPSA 161.0 Open detail RCSB PDB
CAN PDB via homolog Detail RCSB PDB
GAB PDB via homolog Detail RCSB PDB
GBC PDB via homolog Detail RCSB PDB
IF1 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
9QJ RCSB PDB P04181 358.3 Da LogP 1.38 TPSA 161.0 ✓ Ro5 ✓ Clean [H]/N=C/1\C[C@H](C[C@H]1Cc2c(cnc(c2O)C)COP(=O)(…
CAN RCSB PDB P04181 134.1 Da LogP -1.32 TPSA 98.6 ✓ Ro5 ✓ Clean C(CON)[C@@H](C(=O)O)N
GAB RCSB PDB P04181 137.1 Da LogP 0.97 TPSA 63.3 ✓ Ro5 ✓ Clean c1cc(cc(c1)N)C(=O)O
GBC RCSB PDB P04181 141.2 Da LogP 0.51 TPSA 63.3 ✓ Ro5 ✓ Clean C1CC(C=C(C1)C(=O)O)N
IF1 RCSB PDB P04181 488.3 Da LogP 3.32 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/C2C[C@H](C[C@H]2C…
MQ4 RCSB PDB P04181 237.2 Da LogP 1.07 TPSA 80.4 ✓ Ro5 ✓ Clean C1[C@@H](CC(=C1[C@@H](C=O)C(F)(F)F)N)C(=O)O
PFM RCSB PDB P04181 374.3 Da LogP 0.96 TPSA 183.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)\C=C\C(=C\C[C@@H](C(=O…
PMP RCSB PDB B9L0K9 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
POI RCSB PDB Q5SHH5 405.3 Da LogP 0.16 TPSA 178.3 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCCC[C@@H](C(=O)O)NC(…
PPE RCSB PDB Q5SHH5 379.3 Da LogP -0.47 TPSA 187.8 1 viol. ✓ Clean Cc1c(c(c(c[nH+]1)COP(=O)(O)O)CN[C@@H](CCC(=O)O)…
PUT RCSB PDB P42588 88.2 Da LogP -0.32 TPSA 52.0 ✓ Ro5 ✓ Clean C(CCN)CN
VLS RCSB PDB P04181 179.2 Da LogP -2.62 TPSA 110.0 ✓ Ro5 ✓ Clean C(C(=O)O)NC(CO)(CO)CO
Y3D RCSB PDB P04181 372.3 Da LogP 0.56 TPSA 166.6 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@H]2C[C@H](CC2=…

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.