Protein target profile
VK055_2594
deoxyribose-phosphate aldolase
Strong target candidate with converging metabolic, structural and chemical evidence.
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 (%)
- 40.789 Lower values reduce human off-target concern.
- Human E-value
- 7.53e-25
- Gut microbiome similarity
- 2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 34.286 Higher values support similarity to known essential genes.
Localization
- Localization
- Cytoplasmic
Structure confidence
- ColabFold pLDDT
- 96.19 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
Chemistry
Pathways
Sequence
Primary amino-acid sequence viewer.
MTDLKASSLRALKLMDLTTLNDDDTNEKVIALCHQAKTPVGNTAAVCIYPRFIPIARKTLNEQGTPDIRIATVTNFPHGNDDIDIALAETRAAIAYGADEVDVVFPYRALIAGNEQVGFELVKACKEACAAANVLLKVIIETGELKEEALIRKASEISIKAGADFIKTSTGKVPVNATPKSARIMMEVIRDMGVEKTVGFKPAGGVRSAEDAQQFLAIADELFGADWADSRHYRFGASSLLASLLKALGHGDGKSASSY
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
6- GO:0009264 The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
- 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
- GO:0004139 Catalysis of the reaction: 2-deoxy-D-ribose 5-phosphate = D-glyceraldehyde 3-phosphate + acetaldehyde.
- GO:0006018 The chemical reactions and pathways resulting in the breakdown of deoxyribose 1-phosphate, the phosphorylated sugar 1-phospho-2-deoxyribose.
- GO:0016052 The chemical reactions and pathways resulting in the breakdown of carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 1 | 259 | Hamap | MF_00592 | Deoxyribose-phosphate aldolase [deoC]. |
| 1 | 259 | InterPro | IPR023649 | Deoxyribose-phosphate aldolase type II |
| 10 | 246 | SMART | SM01133 | DeoC_2 |
| 10 | 246 | InterPro | IPR002915 | DeoC/FbaB/LacD aldolase |
| 11 | 245 | Pfam | PF01791 | DeoC/LacD family aldolase |
| 11 | 245 | InterPro | IPR002915 | DeoC/FbaB/LacD aldolase |
| 1 | 259 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I |
| 1 | 259 | InterPro | IPR013785 | Aldolase-type TIM barrel |
| 11 | 232 | NCBIfam | TIGR00126 | deoxyribose-phosphate aldolase |
| 11 | 232 | InterPro | IPR011343 | Deoxyribose-phosphate aldolase |
| 1 | 259 | FunFam | G3DSA:3.20.20.70:FF:000034 | Deoxyribose-phosphate aldolase |
| 6 | 246 | SUPERFAMILY | SSF51569 | Aldolase |
| 11 | 225 | CDD | cd00959 | DeoC |
| 11 | 225 | InterPro | IPR011343 | Deoxyribose-phosphate aldolase |
| 5 | 255 | PIRSF | PIRSF001357 | DeoC |
| 5 | 255 | InterPro | IPR011343 | Deoxyribose-phosphate aldolase |
| 5 | 250 | PANTHER | PTHR10889 | DEOXYRIBOSE-PHOSPHATE ALDOLASE |
| 5 | 250 | InterPro | IPR011343 | Deoxyribose-phosphate aldolase |
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
Residue sets
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
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_A0A0H3GIV1
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_2594
|
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 and bioactivity evidence are both 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 |
|---|---|---|---|---|---|---|
| BU2 RCSB PDB | P0A6L0 | 90.1 Da LogP -0.25 TPSA 40.5 | ✓ Ro5 | ✓ Clean |
C[C@@H](CCO)O
|
|
| G3H RCSB PDB | P0A6L0 | 170.1 Da LogP -1.34 TPSA 104.1 | ✓ Ro5 | ✓ Clean |
C([C@H](C=O)O)OP(=O)(O)O
|
|
| HPD RCSB PDB | P0A6L0 | 216.1 Da LogP -1.80 TPSA 127.5 | ✓ Ro5 | ✓ Clean |
C(CO)[C@@H]([C@@H](COP(=O)(O)O)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).
| Ligand | UniProt (homolog) | pchembl | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| CHEMBL4129274 ChEMBL | Q9Y315 | — | 851.5 Da LogP 4.76 TPSA 183.3 | 3 viol. | Alert |
C=CC(=O)Nc1ccccc1Nc1nc(Nc2ccc(N3CCN(CCOCCOCCOCC…
|
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 |
|---|---|---|---|---|---|
| ZINC5975509 ZINC | 0.720 | 202.1 Da LogP -2.19 TPSA 127.5 | ✓ Ro5 | ✓ Clean |
O=P(O)(O)OC[C@H](O)[C@H](O)CO
|
| 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
|
| ZINC2516111 ZINC | 0.667 | 262.2 Da LogP -3.47 TPSA 167.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO
|
| ZINC2522704 ZINC | 0.667 | 262.2 Da LogP -3.47 TPSA 167.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO
|
| ZINC3869812 ZINC | 0.667 | 262.2 Da LogP -3.47 TPSA 167.9 | 1 viol. | ✓ Clean |
O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO
|
| 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
|
| ZINC1532601 ZINC | 0.630 | 200.1 Da LogP -1.98 TPSA 124.3 | ✓ Ro5 | ✓ Clean |
O=C[C@@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC32786787 ZINC | 0.630 | 200.1 Da LogP -1.98 TPSA 124.3 | ✓ Ro5 | ✓ Clean |
O=C[C@H](O)[C@H](O)COP(=O)(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(=…
|
| ZINC1530556 ZINC | 0.586 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC22116391 ZINC | 0.586 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC2522549 ZINC | 0.586 | 214.1 Da LogP -1.59 TPSA 124.3 | ✓ Ro5 | ✓ Clean |
O=CC[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC3606137 ZINC | 0.586 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC3869426 ZINC | 0.586 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C[C@@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC4543673 ZINC | 0.586 | 214.1 Da LogP -1.59 TPSA 124.3 | ✓ Ro5 | ✓ Clean |
O=CC[C@@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC4543675 ZINC | 0.586 | 214.1 Da LogP -1.59 TPSA 124.3 | ✓ Ro5 | ✓ Clean |
O=CC[C@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC4543677 ZINC | 0.586 | 214.1 Da LogP -1.59 TPSA 124.3 | ✓ Ro5 | ✓ Clean |
O=CC[C@@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC8551307 ZINC | 0.586 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC8551308 ZINC | 0.586 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC100065511 ZINC | 0.581 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C(CO)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC100085043 ZINC | 0.581 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C(CO)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC104869937 ZINC | 0.581 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C(CO)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC13537943 ZINC | 0.581 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C(CO)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC85994845 ZINC | 0.581 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O
|
| 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
|
| ZINC100033330 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC100067275 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC100889630 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC104861723 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@@H](O)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O…
|
| ZINC12503760 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@H](O)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC12503763 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@H](O)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC1529626 ZINC | 0.567 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC1532567 ZINC | 0.567 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC1532851 ZINC | 0.567 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O
|
| ZINC19850142 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC2508229 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC30320708 ZINC | 0.567 | 230.1 Da LogP -2.62 TPSA 144.5 | ✓ Ro5 | ✓ Clean |
O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O
|
| ZINC4545927 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)COP(=O)(…
|
| ZINC4545928 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O…
|
| ZINC4545929 ZINC | 0.567 | 260.1 Da LogP -3.26 TPSA 164.8 | 1 viol. | ✓ Clean |
O=C[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)COP(=O)(O…
|
| ZINC5132038 ZINC | 0.563 | 290.2 Da LogP -3.90 TPSA 185.0 | 1 viol. | ✓ Clean |
O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=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
|
| ZINC71842002 ZINC | 0.552 | 445.6 Da LogP 2.04 TPSA 76.7 | ✓ Ro5 | ✓ Clean |
O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NCCCN1CC…
|
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.