Protein profile

PA1010

4-hydroxy-tetrahydrodipicolinate synthase

Genome: NC_002516.2

Gene: PA1010 dapA Structure source: Experimental + AlphaFold UniProt Q9I4W3
Export view
Amino acids 292
Annotations 6
Features 30
PDB binders 8
Druggability 0.897

Overview

Basic information about this protein and its source genome.

Accession
PA1010
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA1010 dapA
Status
annotated
Amino acids
292
Structure source
Experimental + AlphaFold
EC
4.3.3.7
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0008840 Catalysis of the reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H+. 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. GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.293
Human E-value
1.1000000000000002e-28
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 0.897
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0008840 Catalysis of the reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H+.
  • 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.
  • GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
1 292 PIRSF PIRSF001365 DHDPS
1 292 InterPro IPR002220 DapA-like
4 285 CDD cd00950 DHDPS
4 285 InterPro IPR005263 4-hydroxy-tetrahydrodipicolinate synthase, DapA
1 291 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 291 InterPro IPR013785 Aldolase-type TIM barrel
2 285 Pfam PF00701 Dihydrodipicolinate synthetase family
2 285 InterPro IPR002220 DapA-like
1 289 SMART SM01130 DHDPS_2
1 289 InterPro IPR002220 DapA-like
71 89 PRINTS PR00146 Dihydrodipicolinate synthase signature
71 89 InterPro IPR002220 DapA-like
128 145 PRINTS PR00146 Dihydrodipicolinate synthase signature
128 145 InterPro IPR002220 DapA-like
35 56 PRINTS PR00146 Dihydrodipicolinate synthase signature
35 56 InterPro IPR002220 DapA-like
103 119 PRINTS PR00146 Dihydrodipicolinate synthase signature
103 119 InterPro IPR002220 DapA-like
160 180 Coils Coil Coil
1 287 Hamap MF_00418 4-hydroxy-tetrahydrodipicolinate synthase [dapA].
1 287 InterPro IPR005263 4-hydroxy-tetrahydrodipicolinate synthase, DapA
38 55 ProSitePatterns PS00665 Dihydrodipicolinate synthase signature 1.
38 55 InterPro IPR020624 Schiff base-forming aldolase, conserved site
2 289 SUPERFAMILY SSF51569 Aldolase
5 286 NCBIfam TIGR00674 4-hydroxy-tetrahydrodipicolinate synthase
5 286 InterPro IPR005263 4-hydroxy-tetrahydrodipicolinate synthase, DapA
133 163 ProSitePatterns PS00666 Dihydrodipicolinate synthase signature 2.
133 163 InterPro IPR020625 Schiff base-forming aldolase, active site
3 290 PANTHER PTHR12128 DIHYDRODIPICOLINATE SYNTHASE
3 290 InterPro IPR002220 DapA-like

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

6 + 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 3QZE
X-ray 1.59 Å A,B,C,D
100.0% 1-292
PDBe RCSB PDBj File
Viewing
PDB 6P90
X-ray 1.90 Å A,B
100.0% 1-292
PDBe RCSB PDBj File
Loaded
PDB 3PUO
X-ray 2.65 Å A,B
100.0% 1-292
PDBe RCSB PDBj File
Loaded
PDB 3S8H
X-ray 2.70 Å A,B
100.0% 1-292
PDBe RCSB PDBj File
Loaded
PDB 3PS7
X-ray 2.85 Å A,B
100.0% 1-292
PDBe RCSB PDBj File
Loaded
PDB 3NOE
X-ray 2.95 Å A,B
100.0% 1-292
PDBe RCSB PDBj File
Loaded
AlphaFold PA1010
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
2 0.897
3 0.573

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 28.43 0.925
2 1.43 0.018

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

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
3OH
3S8H 2.70 Å Open crystal
90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C(CO)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.