Protein target profile

KP13_01654

Dihydrodipicolinate synthase

Genome: KpKP13 Gene: AHE43824.1 dapA 3D evidence: AlphaFold DB model + ColabFold model UniProt W8UXW6
Length 356
Pocket druggability 0.428
Direct ligand evidence 0 61 total records
Functional annotation 1 EC 3 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
0.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
85.84 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.428
Structure W8UXW6
Pocket Pocket 17
P2Rank 0.841
Structure W8UXW6
Pocket Pocket 1
ColabFold model
FPocket 0.489 · Pocket 7
P2Rank 0.872 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 34 / 4744 genomes with a hit
Prevalence 0.7%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MKPPTGGFFVSVLSLSDTIPASLTPRRFSVNSSLTVNFSFVPGQNDRVLLLSNGLSAQPAGGIMFTGLCAFPLTPLHQQDFDEKAFIRILARLTDAGVDSLGILGSTGSYAYLSREQRRRVVQVAKAHAGSIPMMVGVGAIATNEVLRLVEDAQEAGADALLLPMMSYQPLSAEEIFAFYEEVCRHVSVPVCLYDNPRTTHVMLADELQGRIAALPAIASIKIPGLPAPQASERVAALRQHLPSRVTLGVSGDAWATAGLQAGCEAWYSVCGGLFPRFSLALVRAIRSGDVAQTAALNEQLAPLWRCFDRYGGSLRVIASAAAMLGLCDPDSLPRPLLSLGEEACREVASALRGLA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

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: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+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
16 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
65 352 Pfam PF00701 Dihydrodipicolinate synthetase family
65 352 InterPro IPR002220 DapA-like
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
64 355 SUPERFAMILY SSF51569 Aldolase
70 352 CDD cd00408 DHDPS-like
132 150 PRINTS PR00146 Dihydrodipicolinate synthase signature
132 150 InterPro IPR002220 DapA-like
189 206 PRINTS PR00146 Dihydrodipicolinate synthase signature
189 206 InterPro IPR002220 DapA-like
97 118 PRINTS PR00146 Dihydrodipicolinate synthase signature
97 118 InterPro IPR002220 DapA-like
64 356 SMART SM01130 DHDPS_2
64 356 InterPro IPR002220 DapA-like
61 353 PANTHER PTHR12128 DIHYDRODIPICOLINATE SYNTHASE
61 353 InterPro IPR002220 DapA-like
5 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
21 356 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
64 356 Gene3D G3DSA:3.20.20.70 Aldolase class I
64 356 InterPro IPR013785 Aldolase-type TIM barrel
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #17
0.428
Likely same site as P2Rank 1 2.3 Å 20 shared residues 95% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.841
Likely same site as FPocket 17 2.3 Å 20 shared residues 95% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.035
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_W8UXW6
AlphaFold DB full sequence Viewing
ColabFold KP13_01654
ColabFold full sequence Loaded

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.

61 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2KT PDB via homolog 102.1 Da · LogP 0.05 · TPSA 54.4 Open detail RCSB PDB
3VN PDB via homolog Detail RCSB PDB
GXP PDB via homolog Detail RCSB PDB
GXT PDB via homolog Detail RCSB PDB
GXV PDB via homolog Detail RCSB PDB

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 RCSB PDB D0CFC3 102.1 Da LogP 0.05 TPSA 54.4 ✓ Ro5 ✓ Clean CCC(=O)C(=O)O
3VN RCSB PDB Q9PPB4 318.4 Da LogP -0.41 TPSA 178.7 1 viol. ✓ Clean C(CCN)C[C@@](CC[C@](CCCCN)(C(=O)O)N)(C(=O)O)N
GXP RCSB PDB P75682 146.1 Da LogP -1.41 TPSA 91.7 ✓ Ro5 ✓ Clean C([C@@H](C=O)O)C(=O)C(=O)O
GXT RCSB PDB P75682 58.0 Da LogP -0.62 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)C=O
GXV RCSB PDB P75682 90.1 Da LogP -1.46 TPSA 57.5 ✓ Ro5 ✓ Clean C([C@@H](C=O)O)O
KDG RCSB PDB P75682 178.1 Da LogP -2.26 TPSA 115.1 ✓ Ro5 ✓ Clean C([C@@H]([C@@H](CO)O)O)C(=O)C(=O)O
LYZ RCSB PDB 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 RCSB PDB Q9I6R5 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
OXL RCSB PDB D0CFC3 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
PYR RCSB PDB D0CFC3 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
RSH RCSB PDB P75682 180.2 Da LogP -2.46 TPSA 118.2 ✓ Ro5 ✓ Clean C([C@H]([C@@H](CO)O)O)[C@@H](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.