KpATCC43816 Protein target profile
homoserine dehydrogenase, NAD binding domain protein
Accession: VK055_4120
Target candidate with partial support; inspect missing evidence before prioritizing.
Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.
Main supporting evidence
Risks to review
Evidence coverage
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.
Structure confidence
- ColabFold pLDDT
- 96.66 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelP2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.
Sequence
Primary amino-acid sequence viewer.
MKKVMLIGYGAMAQAVIERLPPQVRVEWIVARESHHAAICLQFGQAVTPLTDPLQCGGTPDLVLECASQQAVAQYGEAVLARGWHLAVISTGALADSELEQRLRQAGGKLTLLAGAVAGIDGLAAAKEGGLERVTYRSRKSPASWRGSYAEQLIDLSAVNEAKIFFEGSAREAARLFPANANVAATIALGGIGLDATRVQLMVDPATQRNTHTLHAEGLFGEFHLELSGLPLASNPKTSTLAALSAVRACRELA
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Enzyme Commission (EC)
1Gene Ontology (GO)
6- GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
- GO:0033735 Catalysis of the reaction: Catalysis of the reaction: L-aspartate + NAD(P)+ + H2O = oxaloacetate + NH4+ + NADPH + H+.
- GO:0009435 The chemical reactions and pathways resulting in the formation of nicotinamide adenine dinucleotide (NAD+), a coenzyme that interconverts with its reduced form, NADH, in many redox and catabolic reactions. NAD+ is derived from various sources including vitamin B3.
- GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
- GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
- GO:0016639 Catalysis of an oxidation-reduction (redox) reaction in which a CH-NH2 group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 8 | 106 | Pfam | PF03447 | Homoserine dehydrogenase, NAD binding domain |
| 8 | 106 | InterPro | IPR005106 | Aspartate/homoserine dehydrogenase, NAD-binding |
| 3 | 252 | PANTHER | PTHR31873 | L-ASPARTATE DEHYDROGENASE-RELATED |
| 160 | 247 | Pfam | PF01958 | Aspartate dehydrogenase, C-terminal |
| 160 | 247 | InterPro | IPR002811 | Aspartate dehydrogenase |
| 116 | 229 | SUPERFAMILY | SSF55347 | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain |
| 16 | 254 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 5 | 251 | Gene3D | G3DSA:3.40.50.720 | - |
| 1 | 15 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 12 | 15 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 1 | 145 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains |
| 1 | 145 | InterPro | IPR036291 | NAD(P)-binding domain superfamily |
| 1 | 254 | PIRSF | PIRSF005227 | Asp_dh_NAD_syn |
| 1 | 254 | InterPro | IPR011182 | L-aspartate dehydrogenase |
| 116 | 234 | Gene3D | G3DSA:3.30.360.10 | Dihydrodipicolinate Reductase; domain 2 |
| 1 | 3 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 2 | 254 | Hamap | MF_01265 | L-aspartate dehydrogenase [nadX]. |
| 2 | 254 | InterPro | IPR020626 | L-aspartate dehydrogenase, prokaryotic |
| 4 | 11 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic 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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Residue sets
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Residue sets
All structural evidence
Structural evidence
0 + 2Experimental 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_A0A0H3GY73
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_4120
|
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.
Only proposed virtual-screening candidates are available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
No PDB ligands found through similar proteins.
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
| Ligand | Tanimoto | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|
| ZINC1532902 ZINC | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC2018106 ZINC | 0.700 | 206.2 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC[C@](O)(CC(=O)O)C(=O)O
|
| ZINC3593496 ZINC | 0.652 | 206.2 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC3593497 ZINC | 0.652 | 206.2 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C[C@](O)(CC(=O)O)C(=O)O
|
| ZINC14686440 ZINC | 0.625 | 436.4 Da LogP -2.64 TPSA 247.9 | 1 viol. | ✓ Clean |
O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…
|
| ZINC14686442 ZINC | 0.625 | 436.4 Da LogP -2.64 TPSA 247.9 | 1 viol. | ✓ Clean |
O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…
|
| ZINC14686444 ZINC | 0.625 | 436.4 Da LogP -2.64 TPSA 247.9 | 1 viol. | ✓ Clean |
O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…
|
| ZINC13398039 ZINC | 0.577 | 234.2 Da LogP -0.38 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O
|
| ZINC2528012 ZINC | 0.577 | 234.2 Da LogP -0.38 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC146315135 ZINC | 0.560 | 204.2 Da LogP 0.86 TPSA 94.8 | ✓ Ro5 | ✓ Clean |
CCCCC[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC146315336 ZINC | 0.560 | 204.2 Da LogP 0.86 TPSA 94.8 | ✓ Ro5 | ✓ Clean |
CCCCC[C@](O)(CC(=O)O)C(=O)O
|
| ZINC1850353 ZINC | 0.556 | 206.1 Da LogP -0.86 TPSA 132.1 | ✓ Ro5 | ✓ Clean |
O=C(O)CC(O)(CC(=O)O)CC(=O)O
|
| ZINC13398014 ZINC | 0.522 | 220.2 Da LogP -1.07 TPSA 110.1 | ✓ Ro5 | ✓ Clean |
COC(=O)CC(O)(CC(=O)OC)C(=O)O
|
| ZINC3861629 ZINC | 0.522 | 206.1 Da LogP -1.16 TPSA 121.1 | ✓ Ro5 | ✓ Clean |
COC(=O)C(O)(CC(=O)O)CC(=O)O
|
| ZINC100969993 ZINC | 0.500 | 359.5 Da LogP 2.70 TPSA 123.9 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCNC(=O)C[C@](O)(CC(=O)O)C(=O)O
|
| ZINC100969996 ZINC | 0.500 | 359.5 Da LogP 2.70 TPSA 123.9 | ✓ Ro5 | ✓ Clean |
CCCCCCCCCCCCNC(=O)C[C@@](O)(CC(=O)O)C(=O)O
|
| ZINC1711854 ZINC | 0.500 | 248.2 Da LogP -0.13 TPSA 149.2 | ✓ Ro5 | ✓ Clean |
O=C(O)CC(CC(=O)O)(CC(=O)O)CC(=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.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.