Protein profile

KP13_02854

Putrescine aminotransferase

Genome: KpKP13

Gene: AHE42577.1 patA Structure source: AlphaFold + ColabFold UniProt A0A0H3GXV4

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Amino acids 459

Annotations 10

Features 28

PDB binders 13

Druggability 0.485

Overview

Basic information about this protein and its source genome.

Accession: KP13_02854
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42577.1 patA
Status: annotated
Amino acids: 459
Structure source: AlphaFold + ColabFold

2.6.1.82 2.6.1.29

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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 33.333
Human E-value: 2.25e-61
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.87

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 0.485

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

Normalized 0.016

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 8 GO

Enzyme Commission (EC)

Gene Ontology (GO)

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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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_A0A0H3GXV4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02854	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
6				0.485
4				0.332
7				0.329

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	Score	Probability
1	6.52	0.33
2	5.41	0.257
3	5.22	0.242
4	5.17	0.239
5	2.84	0.089

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
4				0.378
20				0.355
17				0.346

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	Score	Probability
1	6.66	0.338
2	5.62	0.27
3	4.87	0.218
4	4.81	0.214
5	2.08	0.047

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

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

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
9QJ	5VWO	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	2CAN	P04181	134.1 Da LogP -1.32 TPSA 98.6	✓ Ro5	✓ Clean	`C(CON)[C@@H](C(=O)O)N`
GAB	1GBN	P04181	137.1 Da LogP 0.97 TPSA 63.3	✓ Ro5	✓ Clean	`c1cc(cc(c1)N)C(=O)O`
GBC	1GBN	P04181	141.2 Da LogP 0.51 TPSA 63.3	✓ Ro5	✓ Clean	`C1CC(C=C(C1)C(=O)O)N`
IF1	7JX9	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	6OIA	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	2OAT	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	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`
VLS	7JX9	P04181	179.2 Da LogP -2.62 TPSA 110.0	✓ Ro5	✓ Clean	`C(C(=O)O)NC(CO)(CO)CO`
Y3D	7LK0	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=…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1232972	P04181	8.68	141.2 Da LogP 0.51 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H]1C=C(C(=O)O)CCC1`
CHEMBL220453	P04181	8.38	277.2 Da LogP 2.23 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H]1C[C@@H](C(=O)O)CC1=C(C(F)(F)F)C(F)(F)F`
CHEMBL258218	P04181	—	1050.0 Da LogP 8.07 TPSA 235.0	4 viol.	✓ Clean	`CC(CCCCNC(=O)CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@@H]2…`
CHEMBL330129	P29758	—	127.1 Da LogP -0.19 TPSA 63.3	✓ Ro5	✓ Clean	`C#CC(N)CCC(=O)O`

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1685531	0.875	200.4 Da LogP 2.80 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN`
ZINC34273707	0.875	256.5 Da LogP 4.37 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCCN`
ZINC5178646	0.875	228.4 Da LogP 3.59 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCN`
ZINC4245535	0.769	213.2 Da LogP 2.63 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1cccc(-c2cccc(C(=O)O)c2)c1`
ZINC156685	0.708	212.3 Da LogP 2.08 TPSA 69.1	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)c2cccc(N)c2)c1`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC12505568	0.690	237.3 Da LogP 2.37 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1cccc(C#Cc2cccc(C(=O)O)c2)c1`
ZINC34402619	0.690	229.2 Da LogP 2.76 TPSA 72.5	✓ Ro5	✓ Clean	`Nc1cccc(Oc2cccc(C(=O)O)c2)c1`
ZINC486232	0.677	256.3 Da LogP 2.22 TPSA 92.4	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)Nc2cccc(C(=O)O)c2)c1`
ZINC521400454	0.667	277.3 Da LogP 1.80 TPSA 97.5	✓ Ro5	✓ Clean	`Nc1cccc(S(=O)(=O)c2cccc(C(=O)O)c2)c1`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC1669765	0.633	241.2 Da LogP 2.20 TPSA 80.4	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)c2ccccc2C(=O)O)c1`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC4688104	0.625	256.3 Da LogP 2.22 TPSA 92.4	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)Nc2ccc(C(=O)O)cc2)c1`
ZINC2522309	0.621	213.2 Da LogP 2.63 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1ccc(-c2cccc(C(=O)O)c2)cc1`
ZINC2574116	0.621	213.2 Da LogP 2.63 TPSA 63.3	✓ Ro5	✓ Clean	`Nc1cccc(-c2ccc(C(=O)O)cc2)c1`
ZINC207916	0.600	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)c2cccc(C(=O)O)c2)c1`
ZINC3897007	0.600	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2cccc(C(=O)O)c2)c1`
ZINC141320641	0.581	203.2 Da LogP 2.40 TPSA 43.1	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)CC(F)(F)F)c1`
ZINC291001	0.581	212.3 Da LogP 2.52 TPSA 55.1	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)Nc2ccccc2)c1`
ZINC71456252	0.581	273.3 Da LogP 4.17 TPSA 43.1	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)c2ccc(-c3ccccc3)cc2)c1`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC241850	0.567	348.4 Da LogP 3.29 TPSA 104.6	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)Oc2ccc(OC(=O)c3cccc(N)c3)cc2)c1`
ZINC619156	0.567	346.4 Da LogP 3.36 TPSA 110.2	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)Nc2ccc(NC(=O)c3cccc(N)c3)cc2)c1`
ZINC190579	0.563	204.3 Da LogP 1.89 TPSA 46.3	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)N2CCCCC2)c1`
ZINC7468685	0.563	218.3 Da LogP 2.29 TPSA 46.3	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)N2CCCCCC2)c1`
ZINC90600614	0.563	229.2 Da LogP 2.76 TPSA 72.5	✓ Ro5	✓ Clean	`Nc1cccc(Oc2ccc(C(=O)O)cc2)c1`
ZINC95215251	0.563	229.2 Da LogP 2.76 TPSA 72.5	✓ Ro5	Alert	`Nc1ccc(Oc2cccc(C(=O)O)c2)cc1`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC167226	0.556	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc(I)c1`
ZINC404749	0.556	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1cccc(Br)c1`
ZINC409186	0.556	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)c2ccccc2)c1`
ZINC1600851	0.552	202.1 Da LogP 0.19 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1cccc(P(=O)(O)O)c1`
ZINC65339755	0.552	241.2 Da LogP 2.15 TPSA 80.4	✓ Ro5	✓ Clean	`NC(=O)c1cccc(-c2cccc(C(=O)O)c2)c1`
ZINC188631	0.548	227.3 Da LogP 2.10 TPSA 81.1	✓ Ro5	✓ Clean	`Nc1cccc(NC(=O)c2cccc(N)c2)c1`
ZINC32012507	0.548	211.3 Da LogP 2.81 TPSA 43.1	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)c2cccc(N)c2)cc1`
ZINC32013043	0.548	215.2 Da LogP 2.64 TPSA 43.1	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)c2ccc(F)cc2)c1`
ZINC32016122	0.548	231.7 Da LogP 3.15 TPSA 43.1	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)c2ccc(Cl)cc2)c1`
ZINC32122261	0.548	276.1 Da LogP 3.26 TPSA 43.1	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)c2ccc(Br)cc2)c1`
ZINC75835494	0.548	212.3 Da LogP 2.08 TPSA 69.1	✓ Ro5	Alert	`Nc1cccc(C(=O)c2ccccc2N)c1`
ZINC34552923	0.545	227.3 Da LogP 2.63 TPSA 52.3	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)OCc2ccccc2)c1`
ZINC41042309	0.545	219.2 Da LogP 1.99 TPSA 52.3	✓ Ro5	✓ Clean	`Nc1cccc(C(=O)OCC(F)(F)F)c1`
ZINC96518109	0.545	282.1 Da LogP 1.63 TPSA 77.2	✓ Ro5	✓ Clean	`CS(=O)(=O)C(Cl)(Cl)C(=O)c1cccc(N)c1`
ZINC96518468	0.545	371.1 Da LogP 1.94 TPSA 77.2	✓ Ro5	✓ Clean	`CS(=O)(=O)C(Br)(Br)C(=O)c1cccc(N)c1`

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.