Protein profile

PA2413

diaminobutyrate--2-oxoglutarate aminotransferase

Genome: NC_002516.2

Gene: PA2413 pvdH Structure source: AlphaFold UniProt Q9I168

Export view

Amino acids 469

Annotations 5

Features 21

PDB binders 14

Druggability 0.835

Overview

Basic information about this protein and its source genome.

Accession: PA2413
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA2413 pvdH
Status: annotated
Amino acids: 469
Structure source: AlphaFold

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:0002049 The chemical reactions and pathways resulting in the formation of the siderochrome pyoverdine. 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:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 28.833
Human E-value: 1.5299999999999998e-42
Gut microbiome off-target: hit
Essential (DEG): N
Localization: Cytoplasmic

Selected Druggability evidence

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 0.835

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

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:0002049 The chemical reactions and pathways resulting in the formation of the siderochrome pyoverdine.
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:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
273	310	ProSitePatterns	PS00600	Aminotransferases class-III pyridoxal-phosphate attachment site.
273	310	InterPro	IPR005814	Aminotransferase class-III
145	466	PIRSF	PIRSF000521	Transaminase_4ab_Lys_Orn
145	466	InterPro	IPR005814	Aminotransferase class-III
30	155	PIRSF	PIRSF000521	Transaminase_4ab_Lys_Orn
30	155	InterPro	IPR005814	Aminotransferase class-III
85	354	FunFam	G3DSA:3.40.640.10:FF:000091	Diaminobutyrate--2-oxoglutarate aminotransferase
36	458	Gene3D	G3DSA:3.90.1150.10	Aspartate Aminotransferase, domain 1
36	458	InterPro	IPR015422	Pyridoxal phosphate-dependent transferase, small domain
1	468	PANTHER	PTHR43552	DIAMINOBUTYRATE--2-OXOGLUTARATE AMINOTRANSFERASE
1	468	InterPro	IPR004637	2,4-diaminobutyrate 4-transaminase
32	454	CDD	cd00610	OAT_like
32	454	InterPro	IPR005814	Aminotransferase class-III
32	467	NCBIfam	TIGR00709	diaminobutyrate--2-oxoglutarate transaminase family protein
32	467	InterPro	IPR004637	2,4-diaminobutyrate 4-transaminase
85	354	Gene3D	G3DSA:3.40.640.10	-
85	354	InterPro	IPR015421	Pyridoxal phosphate-dependent transferase, major domain
39	463	SUPERFAMILY	SSF53383	PLP-dependent transferases
39	463	InterPro	IPR015424	Pyridoxal phosphate-dependent transferase
48	463	Pfam	PF00202	Aminotransferase class-III
48	463	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.

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA2413	AlphaFold	—	—	full sequence	—	Viewing

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				0.835
5				0.671
14				0.479
1				0.332

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.

58 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
5PA	1D7R	P16932	332.2 Da LogP 0.41 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNC2(CC2)C(=O)O)O`
ABU	4ATQ	A1R958	103.1 Da LogP -0.19 TPSA 63.3	✓ Ro5	✓ Clean	`C(CC(=O)O)CN`
DCS	1D7S	P16932	333.2 Da LogP -0.78 TPSA 150.2	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]2CONC2=O)O`
ELP	1M0P	P16932	430.3 Da LogP 2.17 TPSA 169.8	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)C=N[C@@](C)(c2ccccc2)P…`
EPC	1M0Q	P16932	354.2 Da LogP 0.65 TPSA 169.8	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\[C@H](C)P(=O)(O)O…`
HCP	1M0N	P16932	394.3 Da LogP 1.57 TPSA 169.8	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)C=NC2(CCCC2)P(=O)(O)O)O`
IK2	1SFF	P22256	322.2 Da LogP -0.19 TPSA 158.4	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNOCC(=O)O)O`
LCS	1D7U	P16932	331.2 Da LogP -0.29 TPSA 150.6	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C/2\CONC2=O)O`
MPM	1M0O	P16932	382.2 Da LogP 1.43 TPSA 169.8	✓ Ro5	✓ Clean	`CC[C@](C)(/N=C/c1c(cnc(c1O)C)COP(=O)(O)O)P(=O)(…`
NMA	1D7V	P16932	334.3 Da LogP 0.66 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)CNC(C)(C)C(=O)O)O`
PMP	1ZC9	P16932	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`

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).

No ChEMBL hits found through similar proteins.

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
ZINC1532708	1.000	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CN)c1O`
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`
ZINC13357569	0.778	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCC(=O)O`
ZINC1532705	0.769	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CO)c1O`
ZINC1656021	0.692	233.2 Da LogP 1.01 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C)c1O`
ZINC1532514	0.643	247.1 Da LogP 0.52 TPSA 117.0	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C=O)c1O`
ZINC1529497	0.588	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045	0.588	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115	0.588	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020	0.588	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440	0.588	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298	0.588	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062	0.588	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC40470158	0.577	216.3 Da LogP 0.49 TPSA 92.4	✓ Ro5	✓ Clean	`NCCCC(=O)NCCCCCC(=O)O`
ZINC78311249	0.565	203.3 Da LogP -0.54 TPSA 92.6	✓ Ro5	✓ Clean	`NCCCN(CCCN)CCC(=O)O`
ZINC13433578	0.550	201.3 Da LogP 1.68 TPSA 80.4	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCC(=O)O`
ZINC201768036	0.542	279.3 Da LogP -0.12 TPSA 100.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCCC(=O)O`
ZINC13377742	0.538	230.4 Da LogP 0.42 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCCNCCCCN`
ZINC1545440	0.538	213.4 Da LogP 4.65 TPSA 26.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCN`
ZINC2385445	0.538	201.4 Da LogP 2.84 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCO`
ZINC34196183	0.538	229.4 Da LogP 3.62 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCO`
ZINC38585283	0.538	203.4 Da LogP 3.39 TPSA 26.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCS`
ZINC38684714	0.538	230.4 Da LogP 0.51 TPSA 81.3	✓ Ro5	✓ Clean	`NCCCCN(CCCCN)CCCCN`
ZINC1703342	0.526	202.2 Da LogP 1.07 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCC(=O)CCCC(=O)O`
ZINC2508031	0.526	230.3 Da LogP 1.85 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCC(=O)CCCCC(=O)O`
ZINC1529994	0.523	219.1 Da LogP -0.02 TPSA 118.6	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(N)n1`
ZINC13526937	0.519	357.5 Da LogP 1.94 TPSA 121.5	✓ Ro5	✓ Clean	`NCCCCCC(=O)NCCCCCC(=O)NCCCCCC(=O)O`
ZINC1532906	0.519	244.3 Da LogP 1.27 TPSA 92.4	✓ Ro5	✓ Clean	`NCCCCCC(=O)NCCCCCC(=O)O`
ZINC2114966	0.519	332.2 Da LogP 0.99 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/CCCC(=O)O)c1O`
ZINC40479778	0.519	272.4 Da LogP 2.05 TPSA 92.4	✓ Ro5	✓ Clean	`NCCCCCCC(=O)NCCCCCCC(=O)O`
ZINC13213450	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@@H]2N[C@H](C(=O)O)CS2)c…`
ZINC13213453	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@H]2N[C@H](C(=O)O)CS2)c1O`
ZINC13213455	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@@H]2N[C@@H](C(=O)O)CS2)…`
ZINC13213457	0.509	350.3 Da LogP 0.49 TPSA 149.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c([C@H]2N[C@@H](C(=O)O)CS2)c…`
ZINC1598087	0.500	215.4 Da LogP 1.61 TPSA 64.1	✓ Ro5	✓ Clean	`NCCCCCCNCCCCCCN`
ZINC26897400	0.500	286.4 Da LogP 3.41 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCCC(=O)O`
ZINC3074813	0.500	258.3 Da LogP 2.63 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCC(=O)CCCCCC(=O)O`
ZINC34423725	0.500	342.5 Da LogP 4.97 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCCCCC(=O)O`
ZINC4822898	0.500	272.3 Da LogP 3.02 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCC(=O)CCCCCC(=O)O`
ZINC4822900	0.500	300.4 Da LogP 3.80 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)CCCCCC(=O)O`
ZINC79832968	0.500	203.2 Da LogP 0.82 TPSA 100.6	✓ Ro5	✓ Clean	`NC(CCCC(=O)O)CCCC(=O)O`
ZINC82505156	0.500	215.3 Da LogP -0.57 TPSA 69.8	✓ Ro5	✓ Clean	`NCCCN1CCN(CCC(=O)O)CC1`

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.