Protein target profile
VK055_0410
beta-D-hydroxybutyrate dehydrogenase
Promising target candidate with multiple supporting evidence streams.
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
- Hit
- Human identity (%)
- 38.202 Lower values reduce human off-target concern.
- Human E-value
- 4.17e-14
- Gut microbiome similarity
- 1.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 38.132 Higher values support similarity to known essential genes.
Localization
- Localization
- Cytoplasmic
Structure confidence
- ColabFold pLDDT
- 96.8 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelThe 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.
Cross-references
External database identifiers for this protein, its structures, ligands, and metabolic reactions.
Sequence
Sequence
Primary amino-acid sequence viewer.
MNLHGKTALVTGSTSGIGLGIAKVLAQAGAQLVLNGFGDSSHARAEVAALGKIPGYHDADLRDVGQIEAMMHYAESTFGGVDIVINNAGIQHVAPVEQFPVDKWNDILAINLSSVFHTTRLALPGMRQRNWGRIINIASVHGLVASKEKSAYVAAKHAVVGLTKTVALETARSGITCNAICPGWVLTPLVQQQIDKRIAEGVDPEQASAQLLAEKQPSGEFVTPQQLGEMALFLCSDAAAQVRGAAWNMDGGWVAQ
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
2- 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:0003858 Catalysis of the reaction: (R)-3-hydroxybutanoate + NAD+ = acetoacetate + H+ + NADH.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 6 | 256 | NCBIfam | TIGR01963 | 3-hydroxybutyrate dehydrogenase |
| 6 | 256 | InterPro | IPR011294 | 3-hydroxybutyrate dehydrogenase |
| 1 | 255 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains |
| 1 | 255 | InterPro | IPR036291 | NAD(P)-binding domain superfamily |
| 139 | 167 | ProSitePatterns | PS00061 | Short-chain dehydrogenases/reductases family signature. |
| 139 | 167 | InterPro | IPR020904 | Short-chain dehydrogenase/reductase, conserved site |
| 1 | 256 | Gene3D | G3DSA:3.40.50.720 | - |
| 79 | 90 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 79 | 90 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 7 | 24 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 7 | 24 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 173 | 190 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 173 | 190 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 152 | 171 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 152 | 171 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 126 | 142 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 126 | 142 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 217 | 237 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 217 | 237 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 1 | 256 | FunFam | G3DSA:3.40.50.720:FF:000084 | Short-chain dehydrogenase reductase |
| 79 | 90 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature |
| 152 | 171 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature |
| 132 | 140 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature |
| 132 | 140 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 12 | 253 | Pfam | PF13561 | Enoyl-(Acyl carrier protein) reductase |
| 1 | 255 | PANTHER | PTHR42879 | 3-OXOACYL-(ACYL-CARRIER-PROTEIN) REDUCTASE |
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 · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
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_A0A0H3GPA8
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_0410
|
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.
Structural ligand evidence is 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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| 3HL RCSB PDB | Q5KST5 | 104.1 Da LogP -0.16 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
C[C@@H](CC(=O)O)O
|
|
| 3HR RCSB PDB | D0VWQ0 | 104.1 Da LogP -0.16 TPSA 57.5 | ✓ Ro5 | ✓ Clean |
C[C@H](CC(=O)O)O
|
|
| AAE RCSB PDB | A0A1E3M3N6 | 102.1 Da LogP 0.05 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CC(=O)CC(=O)O
|
|
| DXX RCSB PDB | D0VWQ0 | 118.1 Da LogP -0.21 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
CC(C(=O)O)C(=O)O
|
|
| EMO RCSB PDB | P16544 | 270.2 Da LogP 1.89 TPSA 94.8 | ✓ Ro5 | Alert |
Cc1cc2c(c(c1)O)C(=O)c3c(cc(cc3O)O)C2=O
|
|
| ISZ RCSB PDB | P16544 | 135.1 Da LogP 1.25 TPSA 66.2 | ✓ Ro5 | Alert |
[H]/N=N/C(=O)c1ccncc1
|
|
| MLA RCSB PDB | D0VWQ0 | 104.1 Da LogP -0.45 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
C(C(=O)O)C(=O)O
|
|
| QT8 RCSB PDB | A0A1E3M3N6 | 116.1 Da LogP 0.44 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CCC(=O)CC(=O)O
|
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 |
|---|---|---|---|---|---|
| ZINC3824868 ZINC | 1.000 | 270.2 Da LogP 1.89 TPSA 94.8 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O)cc(O)c1C2=O
|
| ZINC4095655 ZINC | 0.735 | 284.3 Da LogP 2.19 TPSA 83.8 | ✓ Ro5 | Alert |
COc1cc(O)cc2c1C(=O)c1c(O)cc(C)cc1C2=O
|
| ZINC3978794 ZINC | 0.697 | 284.3 Da LogP 2.19 TPSA 83.8 | ✓ Ro5 | Alert |
COc1cc(O)c2c(c1)C(=O)c1cc(C)cc(O)c1C2=O
|
| ZINC3861630 ZINC | 0.688 | 254.2 Da LogP 2.18 TPSA 74.6 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cccc(O)c1C2=O
|
| ZINC14760847 ZINC | 0.667 | 286.2 Da LogP 1.59 TPSA 115.1 | ✓ Ro5 | Alert |
Cc1cc2c(c(O)c1O)C(=O)c1c(O)cc(O)cc1C2=O
|
| ZINC5277130 ZINC | 0.656 | 238.2 Da LogP 2.48 TPSA 54.4 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)c1ccccc1C2=O
|
| ZINC4098655 ZINC | 0.629 | 304.7 Da LogP 2.54 TPSA 94.8 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O)c(Cl)c(O)c1C2=O
|
| ZINC5461939 ZINC | 0.618 | 286.2 Da LogP 1.59 TPSA 115.1 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1O)C(=O)c1cc(O)cc(O)c1C2=O
|
| ZINC14814143 ZINC | 0.595 | 284.3 Da LogP 2.19 TPSA 83.8 | ✓ Ro5 | Alert |
COc1c(O)ccc2c1C(=O)c1c(O)cc(C)cc1C2=O
|
| ZINC13481200 ZINC | 0.594 | 240.2 Da LogP 1.87 TPSA 74.6 | ✓ Ro5 | Alert |
O=C1c2ccccc2C(=O)c2c(O)cc(O)cc21
|
| ZINC3977762 ZINC | 0.588 | 300.2 Da LogP 1.28 TPSA 132.1 | ✓ Ro5 | Alert |
O=C(O)c1cc(O)c2c(c1)C(=O)c1cc(O)cc(O)c1C2=O
|
| ZINC5812872 ZINC | 0.588 | 286.2 Da LogP 1.07 TPSA 115.1 | ✓ Ro5 | Alert |
O=C1c2cc(O)cc(O)c2C(=O)c2c(O)cc(CO)cc21
|
| ZINC6070245 ZINC | 0.588 | 256.3 Da LogP 2.25 TPSA 77.8 | ✓ Ro5 | ✓ Clean |
Cc1cc(O)c2c(c1)Cc1cc(O)cc(O)c1C2=O
|
| ZINC14760863 ZINC | 0.579 | 300.3 Da LogP 1.90 TPSA 104.1 | ✓ Ro5 | Alert |
COc1c(O)c(C)cc2c1C(=O)c1c(O)cc(O)cc1C2=O
|
| ZINC6070262 ZINC | 0.579 | 314.2 Da LogP 1.59 TPSA 132.1 | ✓ Ro5 | Alert |
Cc1cc2c(c(O)c1C(=O)O)C(=O)c1c(O)cc(O)cc1C2=O
|
| ZINC14819806 ZINC | 0.568 | 314.3 Da LogP 1.50 TPSA 115.1 | ✓ Ro5 | Alert |
C[C@@H](O)Cc1cc(O)c2c(c1)C(=O)c1cc(O)cc(O)c1C2=O
|
| ZINC14819808 ZINC | 0.568 | 314.3 Da LogP 1.50 TPSA 115.1 | ✓ Ro5 | Alert |
C[C@H](O)Cc1cc(O)c2c(c1)C(=O)c1cc(O)cc(O)c1C2=O
|
| ZINC31163880 ZINC | 0.568 | 330.3 Da LogP 0.99 TPSA 135.3 | ✓ Ro5 | Alert |
C[C@@H](O)[C@@H](O)c1cc(O)c2c(c1)C(=O)c1cc(O)cc…
|
| ZINC31163884 ZINC | 0.568 | 330.3 Da LogP 0.99 TPSA 135.3 | ✓ Ro5 | Alert |
C[C@H](O)[C@@H](O)c1cc(O)c2c(c1)C(=O)c1cc(O)cc(…
|
| ZINC31163888 ZINC | 0.568 | 330.3 Da LogP 0.99 TPSA 135.3 | ✓ Ro5 | Alert |
C[C@@H](O)[C@H](O)c1cc(O)c2c(c1)C(=O)c1cc(O)cc(…
|
| ZINC31163892 ZINC | 0.568 | 330.3 Da LogP 0.99 TPSA 135.3 | ✓ Ro5 | Alert |
C[C@H](O)[C@H](O)c1cc(O)c2c(c1)C(=O)c1cc(O)cc(O…
|
| ZINC13334425 ZINC | 0.564 | 268.3 Da LogP 2.48 TPSA 63.6 | ✓ Ro5 | Alert |
COc1cccc2c1C(=O)c1c(O)cc(C)cc1C2=O
|
| ZINC13546016 ZINC | 0.560 | 276.3 Da LogP 0.49 TPSA 110.1 | ✓ Ro5 | ✓ Clean |
C[C@H](O)CC(=O)O[C@@H](C)CC(=O)O[C@@H](C)CC(=O)O
|
| ZINC13546018 ZINC | 0.560 | 276.3 Da LogP 0.49 TPSA 110.1 | ✓ Ro5 | ✓ Clean |
C[C@H](O)CC(=O)O[C@H](C)CC(=O)O[C@@H](C)CC(=O)O
|
| ZINC257400894 ZINC | 0.560 | 276.3 Da LogP 0.49 TPSA 110.1 | ✓ Ro5 | ✓ Clean |
C[C@H](O)CC(=O)O[C@H](C)CC(=O)O[C@H](C)CC(=O)O
|
| ZINC257400895 ZINC | 0.560 | 276.3 Da LogP 0.49 TPSA 110.1 | ✓ Ro5 | ✓ Clean |
C[C@H](O)CC(=O)O[C@@H](C)CC(=O)O[C@H](C)CC(=O)O
|
| ZINC14760819 ZINC | 0.553 | 300.3 Da LogP 1.90 TPSA 104.1 | ✓ Ro5 | Alert |
COc1cc(O)c2c(c1O)C(=O)c1cc(C)cc(O)c1C2=O
|
| ZINC5412537 ZINC | 0.553 | 316.3 Da LogP 1.60 TPSA 124.3 | ✓ Ro5 | Alert |
COc1c(O)c(O)c2c(c1O)C(=O)c1cc(C)cc(O)c1C2=O
|
| ZINC20111521 ZINC | 0.550 | 327.3 Da LogP 1.95 TPSA 98.1 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O)c(CN(C)C)c(O)c1C2=O
|
| ZINC77257242 ZINC | 0.538 | 316.3 Da LogP 1.43 TPSA 124.3 | ✓ Ro5 | Alert |
COCc1c(O)cc2c(c1O)C(=O)c1c(O)cc(O)cc1C2=O
|
| ZINC1637808 ZINC | 0.528 | 267.1 Da LogP 2.36 TPSA 54.4 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)C=C(Br)C2=O
|
| ZINC14811261 ZINC | 0.512 | 300.3 Da LogP 1.37 TPSA 104.1 | ✓ Ro5 | Alert |
COc1cc(CO)cc2c1C(=O)c1c(O)cc(O)cc1C2=O
|
| ZINC137596932 ZINC | 0.510 | 432.4 Da LogP -0.64 TPSA 174.0 | 1 viol. | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O)cc(O[C@H]3O[C@@H](CO…
|
| ZINC2053539354 ZINC | 0.510 | 432.4 Da LogP -0.64 TPSA 174.0 | 1 viol. | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O)cc(O[C@H]3O[C@H](CO)…
|
| ZINC2080144947 ZINC | 0.510 | 432.4 Da LogP -0.64 TPSA 174.0 | 1 viol. | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O)cc(O[C@H]3O[C@H](CO)…
|
| ZINC2080147051 ZINC | 0.510 | 432.4 Da LogP -0.64 TPSA 174.0 | 1 viol. | Alert |
Cc1cc(O[C@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2O…
|
| ZINC238733159 ZINC | 0.510 | 432.4 Da LogP -0.64 TPSA 174.0 | 1 viol. | Alert |
Cc1cc(O[C@H]2O[C@@H](CO)[C@H](O)[C@@H](O)[C@@H]…
|
| ZINC238774329 ZINC | 0.510 | 432.4 Da LogP -0.64 TPSA 174.0 | 1 viol. | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O)cc(O[C@@H]3O[C@H](CO…
|
| ZINC253593197 ZINC | 0.510 | 432.4 Da LogP -0.64 TPSA 174.0 | 1 viol. | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O)cc(O[C@@H]3O[C@@H](C…
|
| ZINC253598174 ZINC | 0.510 | 432.4 Da LogP -0.64 TPSA 174.0 | 1 viol. | Alert |
Cc1cc(O[C@@H]2O[C@@H](CO)[C@H](O)[C@@H](O)[C@@H…
|
| ZINC33832450 ZINC | 0.510 | 432.4 Da LogP -0.64 TPSA 174.0 | 1 viol. | Alert |
Cc1cc(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@H]2…
|
| ZINC4098672 ZINC | 0.510 | 432.4 Da LogP -0.64 TPSA 174.0 | 1 viol. | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O)cc(O[C@@H]3O[C@H](CO…
|
| ZINC14814264 ZINC | 0.500 | 416.4 Da LogP 0.39 TPSA 153.8 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O[C@@H]3O[C@H](C)[C@@H…
|
| ZINC14814268 ZINC | 0.500 | 416.4 Da LogP 0.39 TPSA 153.8 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O[C@H]3O[C@H](C)[C@@H]…
|
| ZINC2332918206 ZINC | 0.500 | 388.8 Da LogP 2.98 TPSA 107.0 | ✓ Ro5 | Alert |
CC(=O)Oc1cc2c(c(OC(C)=O)c1Cl)C(=O)c1c(O)cc(C)cc…
|
| ZINC253477263 ZINC | 0.500 | 416.4 Da LogP 0.39 TPSA 153.8 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O[C@@H]3O[C@H](C)[C@H]…
|
| ZINC31425373 ZINC | 0.500 | 416.4 Da LogP 0.39 TPSA 153.8 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O[C@H]3O[C@@H](C)[C@H]…
|
| ZINC4098673 ZINC | 0.500 | 416.4 Da LogP 0.39 TPSA 153.8 | ✓ Ro5 | Alert |
Cc1cc(O)c2c(c1)C(=O)c1cc(O[C@@H]3O[C@@H](C)[C@H…
|
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.