Protein profile

PA3659

succinyldiaminopimelate transaminase

Genome: NC_002516.2

Gene: PA3659 Structure source: AlphaFold UniProt Q9HXY0
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Amino acids 402
Annotations 6
Features 12
PDB binders 9
Druggability 0.891

Overview

Basic information about this protein and its source genome.

Accession
PA3659
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3659
Status
annotated
Amino acids
402
Structure source
AlphaFold
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:0009016 Catalysis of the reaction: N-succinyl-(2S,6S)-2,6-diaminopimelate + 2-oxoglutarate = (S)-2-succinylamino-6-oxoheptanedioate + L-glutamate. GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid. GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate. 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 (%)
26.689
Human E-value
4.58e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
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 0.891
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • 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:0009016 Catalysis of the reaction: N-succinyl-(2S,6S)-2,6-diaminopimelate + 2-oxoglutarate = (S)-2-succinylamino-6-oxoheptanedioate + L-glutamate.
  • GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
  • GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
  • 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.

12 records
Show feature table
Start End DB Term Name
32 395 Pfam PF00155 Aminotransferase class I and II
32 395 InterPro IPR004839 Aminotransferase, class I/classII
1 398 NCBIfam TIGR03538 succinyldiaminopimelate transaminase
1 398 InterPro IPR019878 Succinyldiaminopimelate transaminase, DapC, beta/gammaproteobacteria
2 400 SUPERFAMILY SSF53383 PLP-dependent transferases
2 400 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
8 383 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
8 383 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
32 397 CDD cd00609 AAT_like
5 400 PANTHER PTHR42832 AMINO ACID AMINOTRANSFERASE
43 296 Gene3D G3DSA:3.40.640.10 -
43 296 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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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 PA3659
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
1 0.891

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.

59 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
AKG
5WMI
Q9SIE1 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
BO3
5WMK
Q9SIE1 61.8 Da LogP -2.05 TPSA 60.7 ✓ Ro5 ✓ Clean B(O)(O)O
HCI
1V2F
Q75WK2 150.2 Da LogP 1.70 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)CCC(=O)O
KMT
1V2E
Q75WK2 148.2 Da LogP 0.39 TPSA 54.4 ✓ Ro5 ✓ Clean CSCCC(=O)C(=O)O
MAE
1BKG
Q56232 116.1 Da LogP -0.29 TPSA 74.6 ✓ Ro5 ✓ Clean C(=C/C(=O)O)/C(=O)O
MLI
5WMK
Q9SIE1 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
N5F
3CBF
Q72LL6 392.3 Da LogP 0.50 TPSA 186.5 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCCC(=O)O)C(=…
PGU
2ZYJ
Q72LL6 378.3 Da LogP 0.11 TPSA 186.5 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCC(=O)O)C(=O…
PMP
6L1O
P39643 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)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.