Protein profile

PA3666

2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase

Genome: NC_002516.2

Gene: dapD PA3666 Structure source: Experimental + AlphaFold UniProt G3XD76
Export view
Amino acids 344
Annotations 6
Features 18
PDB binders 4
Druggability 0.748

Overview

Basic information about this protein and its source genome.

Accession
PA3666
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
dapD PA3666
Status
annotated
Amino acids
344
Structure source
Experimental + AlphaFold
EC
2.3.1.117
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0008666 Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + H2O + succinyl-CoA = L-2-succinylamino-6-oxopimelate + CoA. GO:0000287 Binding to a magnesium (Mg) ion. GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls. GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Unknown

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 0.748
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MSQSLFSLAFGVGTQNRQEAWLEVFYALPLLKPSSEIVAAVAPILGYAAGNQALTFTSQQAYQLADALKGIDAAQSALLSRLAESQKPLVATLLAEDAAPSSTAEAYLKLHLLSHRLVKPHAVNLSGIFPLLPNVAWTNIGAVDLAELAELQLEARLKGKLLEVFSVDKFPKMTDYVVPAGVRIADTARVRLGAYIGEGTTVMHEGFVNFNAGTEGPGMIEGRVSAGVFVGKGSDLGGGCSTMGTLSGGGNIVISVGEGCLIGANAGIGIPLGDRNIVEAGLYITAGTKVALLDEQNALVKVVKARDLAGQPDLLFRRNSQNGAVECKTNKTAIELNEALHAHN

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0008666 Catalysis of the reaction: (S)-2,3,4,5-tetrahydrodipicolinate + H2O + succinyl-CoA = L-2-succinylamino-6-oxopimelate + CoA.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0019877 OBSOLETE. The chemical reactions and pathways resulting in the formation of diaminopimelate, both as an intermediate in lysine biosynthesis and as a component (as meso-diaminopimelate) of the peptidoglycan of Gram-negative bacterial cell walls.
  • GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.

Sequence Features

Domain/signature hits from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
254 286 Pfam PF14602 Hexapeptide repeat of succinyl-transferase
254 286 InterPro IPR001451 Hexapeptide repeat
4 341 Hamap MF_02122 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase [dapD].
4 341 InterPro IPR026586 Type 2 tetrahydrodipicolinate N-succinyltransferase family
132 172 FunFam G3DSA:3.30.60.70:FF:000001 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
132 172 Pfam PF14789 Tetrahydrodipicolinate N-succinyltransferase middle
132 172 InterPro IPR032784 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain
181 327 CDD cd04649 LbH_THP_succinylT_putative
173 344 Gene3D G3DSA:2.160.10.10 Hexapeptide repeat proteins
1 131 Gene3D G3DSA:3.30.70.2010 -
82 129 Pfam PF14790 Tetrahydrodipicolinate N-succinyltransferase N-terminal
5 344 NCBIfam TIGR03536 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
5 344 InterPro IPR019876 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, gammaproteobacteria
132 172 Gene3D G3DSA:3.30.60.70 -
132 172 InterPro IPR038361 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase, middle domain superfamily
173 344 FunFam G3DSA:2.160.10.10:FF:000009 2,3,4,5-tetrahydropyridine-2,6-dicarboxylate N-succinyltransferase
97 306 SUPERFAMILY SSF51161 Trimeric LpxA-like enzymes
97 306 InterPro IPR011004 Trimeric LpxA-like superfamily

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

Loading 3D structure...

Legend High Medium Low

Structural evidence

4 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 3R5D
X-ray 1.80 Å A,B,C,D,E,F
100.0% 1-344
PDBe RCSB PDBj File
Viewing
PDB 3R5A
X-ray 1.89 Å A,B,C,D,E,F
100.0% 1-344
PDBe RCSB PDBj File
Loaded
PDB 3R5C
X-ray 2.40 Å A,B,C
100.0% 1-344
PDBe RCSB PDBj File
Loaded
PDB 3R5B
X-ray 2.51 Å A,B,C,D,E,F
100.0% 1-344
PDBe RCSB PDBj File
Loaded
AlphaFold PA3666
AlphaFold — — 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
1 0.748

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 6.19 0.309
2 2.39 0.064
3 1.97 0.041
4 1.25 0.012

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.

54 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.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
NPI
3R5B 2.51 Å Open crystal
175.2 Da LogP 0.04 TPSA 100.6 ✓ Ro5 ✓ Clean C(CCC(=O)O)C[C@@H](C(=O)O)N
P0A
3R5A 1.89 Å Open crystal
175.2 Da LogP 0.04 TPSA 100.6 ✓ Ro5 ✓ Clean C(CCC(=O)O)C[C@H](C(=O)O)N
SIN
3R5C 2.40 Å Open crystal
118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)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.