Protein profile

KP13_05269

putative dihydrodipicolinate synthase

Genome: KpKP13

Gene: AHE44676.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GN51
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Amino acids 294
Annotations 3
Features 27
PDB binders 6
Druggability 0.283

Overview

Basic information about this protein and its source genome.

Accession
KP13_05269
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE44676.1
Status
annotated
Amino acids
294
Structure source
AlphaFold + ColabFold
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:0008840 Catalysis of the reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H+. GO:0044281 The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
28.761
Human E-value
3.78e-18
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.39

Selected Druggability evidence

AlphaFold / UniProt model

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 0.283
Structure A0A0H3GN51
Pocket Pocket 1
P2Rank 0.758
Structure A0A0H3GN51
Pocket Pocket 1
ColabFold model
FPocket 0.389 · Pocket 1
P2Rank 0.622 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 24 / 4744 genomes with a hit
Normalized 0.005

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • 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:0008840 Catalysis of the reaction: L-aspartate 4-semialdehyde + pyruvate = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O + H+.
  • GO:0044281 The chemical reactions and pathways involving small molecules, any low molecular weight, monomeric, non-encoded molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
21 294 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
4 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
135 165 ProSitePatterns PS00666 Dihydrodipicolinate synthase signature 2.
135 165 InterPro IPR020625 Schiff base-forming aldolase, active site
15 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 291 PIRSF PIRSF001365 DHDPS
1 291 InterPro IPR002220 DapA-like
2 285 SUPERFAMILY SSF51569 Aldolase
105 121 PRINTS PR00146 Dihydrodipicolinate synthase signature
105 121 InterPro IPR002220 DapA-like
37 58 PRINTS PR00146 Dihydrodipicolinate synthase signature
37 58 InterPro IPR002220 DapA-like
130 147 PRINTS PR00146 Dihydrodipicolinate synthase signature
130 147 InterPro IPR002220 DapA-like
73 91 PRINTS PR00146 Dihydrodipicolinate synthase signature
73 91 InterPro IPR002220 DapA-like
4 293 SMART SM01130 DHDPS_2
4 293 InterPro IPR002220 DapA-like
8 272 CDD cd00408 DHDPS-like
1 294 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 294 InterPro IPR013785 Aldolase-type TIM barrel
4 267 PANTHER PTHR12128 DIHYDRODIPICOLINATE SYNTHASE
4 267 InterPro IPR002220 DapA-like
5 287 Pfam PF00701 Dihydrodipicolinate synthetase family
5 287 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

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Structural evidence

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GN51
AlphaFold — — full sequence — Viewing
ColabFold KP13_05269
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 0.283

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 10.05 0.541
2 3.26 0.113
3 1.32 0.015

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.

56 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
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
MLT
3IRD
A5I6N2 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)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

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.