Protein profile

VK055_3967

putrescine aminotransferase

Genome: KpATCC43816

Gene: AIK82515.1 ygjG Structure source: AlphaFold + ColabFold UniProt A0A4P0YGS4
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Amino acids 332
Annotations 7
Features 21
PDB binders 5
Druggability 0.288

Overview

Basic information about this protein and its source genome.

Accession
VK055_3967
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK82515.1 ygjG
Status
annotated
Amino acids
332
Structure source
AlphaFold + ColabFold
EC
2.6.1.82
GO
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: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: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:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid. 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:0042802 Binding to an identical protein or proteins.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
35.897
Human E-value
5.51e-55
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
42.574
DEG E-value
2.96e-59
Localization
Cytoplasmic
ColabFold pLDDT
98.16

Selected Druggability evidence

AlphaFold / UniProt model

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 0.288
Structure A0A4P0YGS4
Pocket Pocket 2
P2Rank 0.296
Structure A0A4P0YGS4
Pocket Pocket 1
ColabFold model
FPocket 0.702 · Pocket 2
P2Rank 0.188 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 79 / 4744 genomes with a hit
Normalized 0.017

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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: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: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:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
  • 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:0042802 Binding to an identical protein or proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
2 226 Gene3D G3DSA:3.40.640.10 -
2 226 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
1 226 FunFam G3DSA:3.40.640.10:FF:000004 Acetylornithine aminotransferase
2 313 CDD cd00610 OAT_like
2 313 InterPro IPR005814 Aminotransferase class-III
41 325 PIRSF PIRSF000521 Transaminase_4ab_Lys_Orn
41 325 InterPro IPR005814 Aminotransferase class-III
1 49 PIRSF PIRSF000521 Transaminase_4ab_Lys_Orn
1 49 InterPro IPR005814 Aminotransferase class-III
2 323 SUPERFAMILY SSF53383 PLP-dependent transferases
2 323 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
2 322 Pfam PF00202 Aminotransferase class-III
2 322 InterPro IPR005814 Aminotransferase class-III
227 316 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
227 316 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
2 325 PANTHER PTHR11986 AMINOTRANSFERASE CLASS III
1 322 NCBIfam TIGR03372 putrescine aminotransferase
1 322 InterPro IPR017747 Putrescine aminotransferase
308 328 Coils Coil Coil
141 178 ProSitePatterns PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.
141 178 InterPro IPR005814 Aminotransferase class-III

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

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A4P0YGS4
AlphaFold — — full sequence — Viewing
ColabFold VK055_3967
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
5 0.033
1 0.022
9 0.006
4 0.002

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 6.87 0.296
2 5.79 0.233
3 4.6 0.164
4 2.06 0.038
5 1.8 0.028

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.

56 records

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
PMP
6IO1
B9L0K9 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
POI
1WKG
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
1WKH
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
4UOX
P42588 88.2 Da LogP -0.32 TPSA 52.0 ✓ Ro5 ✓ Clean C(CCN)CN
SUO
4ADD
P77581 232.2 Da LogP -0.84 TPSA 129.7 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)NC(=O)CCC(=O)O)CN

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.