Protein profile

VK055_4699

dihydrodipicolinate synthase

Genome: KpATCC43816

Gene: dapA AIK83233.1 Structure source: Experimental + ColabFold UniProt W9BBZ5
Export view
Amino acids 280
Annotations 6
Features 29
PDB binders 7
Druggability 0.574

Overview

Basic information about this protein and its source genome.

Accession
VK055_4699
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
dapA AIK83233.1
Status
annotated
Amino acids
280
Structure source
Experimental + ColabFold
EC
4.3.3.7
GO
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. GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate. GO:0008840 Catalysis of the reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H+. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.167
Human E-value
3.67e-22
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
91.786
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
98.77

Selected Druggability evidence

PDB experimental structure

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 0.574
Structure 6UE0
Pocket Pocket 1
P2Rank 0.787
Structure 6UE0
Pocket Pocket 1
ColabFold model
FPocket 0.968 · Pocket 4
P2Rank 0.982 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 182 / 4744 genomes with a hit
Normalized 0.038

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: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.
  • GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
  • GO:0008840 Catalysis of the reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H+.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
121 151 ProSitePatterns PS00666 Dihydrodipicolinate synthase signature 2.
121 151 InterPro IPR020625 Schiff base-forming aldolase, active site
26 43 ProSitePatterns PS00665 Dihydrodipicolinate synthase signature 1.
26 43 InterPro IPR020624 Schiff base-forming aldolase, conserved site
1 276 Pfam PF00701 Dihydrodipicolinate synthetase family
1 276 InterPro IPR002220 DapA-like
1 276 Hamap MF_00418 4-hydroxy-tetrahydrodipicolinate synthase [dapA].
1 276 InterPro IPR005263 4-hydroxy-tetrahydrodipicolinate synthase, DapA
2 279 PANTHER PTHR12128 DIHYDRODIPICOLINATE SYNTHASE
2 279 InterPro IPR002220 DapA-like
1 276 NCBIfam TIGR00674 4-hydroxy-tetrahydrodipicolinate synthase
59 77 PRINTS PR00146 Dihydrodipicolinate synthase signature
59 77 InterPro IPR002220 DapA-like
91 107 PRINTS PR00146 Dihydrodipicolinate synthase signature
91 107 InterPro IPR002220 DapA-like
116 133 PRINTS PR00146 Dihydrodipicolinate synthase signature
116 133 InterPro IPR002220 DapA-like
23 44 PRINTS PR00146 Dihydrodipicolinate synthase signature
23 44 InterPro IPR002220 DapA-like
1 280 SUPERFAMILY SSF51569 Aldolase
1 280 PIRSF PIRSF001365 DHDPS
1 280 InterPro IPR002220 DapA-like
1 280 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 280 InterPro IPR013785 Aldolase-type TIM barrel
1 278 SMART SM01130 DHDPS_2
1 278 InterPro IPR002220 DapA-like
1 280 FunFam G3DSA:3.20.20.70:FF:000046 4-hydroxy-tetrahydrodipicolinate synthase
1 274 CDD cd00950 DHDPS
1 274 InterPro IPR005263 4-hydroxy-tetrahydrodipicolinate synthase, DapA

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

1 + 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 6UE0
X-ray 1.89 Å AAA,BBB
100.0% 1-280
PDBe RCSB PDBj File
Viewing
ColabFold VK055_4699
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
1 0.319
5 0.249
20 0.247

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 37.02 0.957
2 10.24 0.55
3 9.41 0.506
4 1.29 0.014
5 1.13 0.008

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

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
2KT
3TDF
D0CFC3 102.1 Da LogP 0.05 TPSA 54.4 ✓ Ro5 ✓ Clean CCC(=O)C(=O)O
3OH
3S8H
Q9I4W3 90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C(CO)C(=O)O
FLC
4PFM
A9DKW4 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
LYZ
3TCE
D0CFC3 162.2 Da LogP -1.50 TPSA 109.6 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)[C@H](CN)O
OXL
3U8G
D0CFC3 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
PYR
3RK8
D0CFC3 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
TLA
5T26
P0A6L2 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)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.