Target candidate with partial support; inspect missing evidence before prioritizing.
3 signalsStrengths
Risks / watch
How to read 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 TPW 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.
Overview
Basic information about this protein and its source genome.
- Accession
- PA4089
- Gene
- PA4089
- Status
- annotated
- Amino acids
- 253
- 3D evidence
- AlphaFold DB model
Target profile
Computed evidence for target prioritization.
- Human off-target
- Hit
- Human identity (%)
- 41.935
- Human E-value
- 6.59e-10
- Gut microbiome off-target
- Hit
- Essential (DEG)
- Y
- Localization
- Cytoplasmic
Selected pocket evidence
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.
Sequence
Primary amino-acid sequence viewer.
MRRLENRVALVTGAGQGIGRAIAECFAAEGARVLLATRTASRGQAVLEAIRLGGGTAELLAVDLSEYDAARRAVSATLERFGQLDILLHNAAAFPQCALAELDEGTLERTLAVNLKSCFRLTQAALPALRRSVAGRVLVTSSVTGPRTAIPGLSHYAASKAGVNGFIRAAALELAGDGITVNGVEPGLVATPALGSLGDAAALAAHIPLGRVGQPLDIAHAMLFLASDEASYITGQTLVVDGGALLPENGGLA
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
1- 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.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 1 | 27 | Phobius | SIGNAL_PEPTIDE | Signal peptide region |
| 1 | 7 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. |
| 82 | 93 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature |
| 82 | 93 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 135 | 143 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature |
| 135 | 143 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 156 | 175 | PRINTS | PR00080 | Short-chain dehydrogenase/reductase (SDR) superfamily signature |
| 156 | 175 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 7 | 187 | SMART | SM00822 | This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group. |
| 5 | 245 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains |
| 5 | 245 | InterPro | IPR036291 | NAD(P)-binding domain superfamily |
| 13 | 243 | Pfam | PF13561 | Enoyl-(Acyl carrier protein) reductase |
| 28 | 253 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. |
| 2 | 245 | PANTHER | PTHR43639 | OXIDOREDUCTASE, SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY (AFU_ORTHOLOGUE AFUA_5G02870) |
| 1 | 248 | FunFam | G3DSA:3.40.50.720:FF:000084 | Short-chain dehydrogenase reductase |
| 129 | 145 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 129 | 145 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 156 | 175 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 82 | 93 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 8 | 25 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 8 | 25 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 208 | 228 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 208 | 228 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 177 | 194 | PRINTS | PR00081 | Glucose/ribitol dehydrogenase family signature |
| 177 | 194 | InterPro | IPR002347 | Short-chain dehydrogenase/reductase SDR |
| 143 | 171 | ProSitePatterns | PS00061 | Short-chain dehydrogenases/reductases family signature. |
| 143 | 171 | InterPro | IPR020904 | Short-chain dehydrogenase/reductase, conserved site |
| 1 | 246 | Gene3D | G3DSA:3.40.50.720 | - |
| 20 | 27 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. |
| 8 | 19 | 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.
Loading 3D structure...
Structural evidence
0 + 1Experimental 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
PA4089
|
AlphaFold DB | — | — | full sequence | — | Viewing |
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Inspect mode shows the specific pocket/cavity and hides other active pocket layers. Use Surface when you need the wider residue environment.
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
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 TPW, 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 |
|---|---|---|---|---|---|---|
| F3V RCSB PDB | A0QP46 | 73.1 Da LogP -0.47 TPSA 43.1 | ✓ Ro5 | ✓ Clean |
CC(=O)CN
|
|
| MLH RCSB PDB | V5VHN7 | 417.3 Da LogP 4.34 TPSA 54.7 | ✓ Ro5 | ✓ Clean |
CCOC(=O)c1c2cc(c(cc2n(c1CN(C)C)c3ccccc3)Br)O
|
|
| PG5 RCSB PDB | B1MJ88 | 178.2 Da LogP 0.31 TPSA 36.9 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOC
|
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 |
|---|---|---|---|---|---|---|
| KDH ChEMBL | Q8I2S7 | 6.50 | 458.4 Da LogP 2.23 TPSA 197.4 | 2 viol. | Alert |
c1c(cc(c(c1O)O)O)[C@@H]2[C@@H](Cc3c(cc(cc3O2)O)…
|
| LU2 ChEMBL | Q965D6 | 6.10 | 286.2 Da LogP 2.28 TPSA 111.1 | ✓ Ro5 | Alert |
c1cc(c(cc1C2=CC(=O)c3c(cc(cc3O2)O)O)O)O
|
| CHEMBL129451 ChEMBL | Q965D6 | 6.00 | 442.4 Da LogP 2.53 TPSA 177.1 | 1 viol. | Alert |
O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1ccc(O)c(O)c…
|
| CHEMBL36327 ChEMBL | Q965D6 | 6.00 | 442.4 Da LogP 2.53 TPSA 177.1 | 1 viol. | Alert |
O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)…
|
| NAR ChEMBL | Q965D6 | — | 272.3 Da LogP 2.51 TPSA 87.0 | ✓ Ro5 | ✓ Clean |
c1cc(ccc1[C@@H]2CC(=O)c3c(cc(cc3O2)O)O)O
|
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 |
|---|---|---|---|---|---|
| ZINC1233995 ZINC | 1.000 | 417.3 Da LogP 4.34 TPSA 54.7 | ✓ Ro5 | ✓ Clean |
CCOC(=O)c1c(CN(C)C)n(-c2ccccc2)c2cc(Br)c(O)cc12
|
| ZINC156701 ZINC | 1.000 | 272.3 Da LogP 2.51 TPSA 87.0 | ✓ Ro5 | ✓ Clean |
O=C1C[C@@H](c2ccc(O)cc2)Oc2cc(O)cc(O)c21
|
| ZINC1692489 ZINC | 1.000 | 222.3 Da LogP 0.33 TPSA 46.2 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOC
|
| ZINC1785 ZINC | 1.000 | 272.3 Da LogP 2.51 TPSA 87.0 | ✓ Ro5 | ✓ Clean |
O=C1C[C@H](c2ccc(O)cc2)Oc2cc(O)cc(O)c21
|
| ZINC18185774 ZINC | 1.000 | 286.2 Da LogP 2.28 TPSA 111.1 | ✓ Ro5 | Alert |
O=c1cc(-c2ccc(O)c(O)c2)oc2cc(O)cc(O)c12
|
| ZINC3870412 ZINC | 1.000 | 458.4 Da LogP 2.23 TPSA 197.4 | 2 viol. | Alert |
O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c…
|
| ZINC3870413 ZINC | 1.000 | 458.4 Da LogP 2.23 TPSA 197.4 | 2 viol. | Alert |
O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(…
|
| ZINC3870414 ZINC | 1.000 | 458.4 Da LogP 2.23 TPSA 197.4 | 2 viol. | Alert |
O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c(…
|
| ZINC3870415 ZINC | 1.000 | 458.4 Da LogP 2.23 TPSA 197.4 | 2 viol. | Alert |
O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(O…
|
| ZINC4530388 ZINC | 1.000 | 266.3 Da LogP 0.35 TPSA 55.4 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOC
|
| ZINC5701172 ZINC | 1.000 | 310.4 Da LogP 0.36 TPSA 64.6 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOC
|
| ZINC5997861 ZINC | 1.000 | 398.5 Da LogP 0.40 TPSA 83.1 | ✓ Ro5 | ✓ Clean |
COCCOCCOCCOCCOCCOCCOCCOCCOC
|
| ZINC14436185 ZINC | 0.854 | 472.4 Da LogP 2.54 TPSA 186.4 | 2 viol. | Alert |
COc1cc(C(=O)O[C@@H]2Cc3c(O)cc(O)cc3O[C@@H]2c2cc…
|
| ZINC3978503 ZINC | 0.851 | 442.4 Da LogP 2.53 TPSA 177.1 | 1 viol. | Alert |
O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)…
|
| ZINC4534390 ZINC | 0.851 | 442.4 Da LogP 2.53 TPSA 177.1 | 1 viol. | Alert |
O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)c(O)c…
|
| ZINC4544252 ZINC | 0.851 | 442.4 Da LogP 2.53 TPSA 177.1 | 1 viol. | Alert |
O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1ccc(O)c(O)c1…
|
| ZINC8681494 ZINC | 0.851 | 442.4 Da LogP 2.53 TPSA 177.1 | 1 viol. | Alert |
O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1ccc(O)c(O)c…
|
| ZINC8453886 ZINC | 0.849 | 431.3 Da LogP 4.65 TPSA 54.7 | ✓ Ro5 | ✓ Clean |
CCOC(=O)c1c(CN(C)C)n(-c2ccc(C)cc2)c2cc(Br)c(O)c…
|
| ZINC14727965 ZINC | 0.848 | 426.4 Da LogP 2.82 TPSA 156.9 | 1 viol. | Alert |
O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1ccc(O)cc1)…
|
| ZINC4935 ZINC | 0.816 | 256.3 Da LogP 2.80 TPSA 66.8 | ✓ Ro5 | ✓ Clean |
O=C1C[C@H](c2ccccc2)Oc2cc(O)cc(O)c21
|
| ZINC73693 ZINC | 0.816 | 256.3 Da LogP 2.80 TPSA 66.8 | ✓ Ro5 | ✓ Clean |
O=C1C[C@@H](c2ccccc2)Oc2cc(O)cc(O)c21
|
| ZINC14728393 ZINC | 0.806 | 288.3 Da LogP 2.22 TPSA 107.2 | ✓ Ro5 | ✓ Clean |
O=C1C[C@@H](c2cc(O)cc(O)c2)Oc2cc(O)cc(O)c21
|
| ZINC5222178 ZINC | 0.800 | 431.3 Da LogP 4.64 TPSA 43.7 | ✓ Ro5 | ✓ Clean |
CCOC(=O)c1c(CN(C)C)n(-c2ccccc2)c2cc(Br)c(OC)cc12
|
| ZINC58116 ZINC | 0.795 | 288.3 Da LogP 2.22 TPSA 107.2 | ✓ Ro5 | Alert |
O=C1C[C@H](c2ccc(O)c(O)c2)Oc2cc(O)cc(O)c21
|
| ZINC58117 ZINC | 0.795 | 288.3 Da LogP 2.22 TPSA 107.2 | ✓ Ro5 | Alert |
O=C1C[C@@H](c2ccc(O)c(O)c2)Oc2cc(O)cc(O)c21
|
| ZINC3871576 ZINC | 0.778 | 270.2 Da LogP 2.58 TPSA 90.9 | ✓ Ro5 | ✓ Clean |
O=c1cc(-c2ccc(O)cc2)oc2cc(O)cc(O)c12
|
| ZINC4348965 ZINC | 0.775 | 270.3 Da LogP 3.11 TPSA 66.8 | ✓ Ro5 | ✓ Clean |
Cc1cc(O)c2c(c1)O[C@H](c1ccc(O)cc1)CC2=O
|
| ZINC4348970 ZINC | 0.775 | 270.3 Da LogP 3.11 TPSA 66.8 | ✓ Ro5 | ✓ Clean |
Cc1cc(O)c2c(c1)O[C@@H](c1ccc(O)cc1)CC2=O
|
| ZINC21992193 ZINC | 0.760 | 458.4 Da LogP 2.23 TPSA 197.4 | 2 viol. | Alert |
O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c…
|
| ZINC21992196 ZINC | 0.760 | 458.4 Da LogP 2.23 TPSA 197.4 | 2 viol. | Alert |
O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@@H]1c1cc(O)c(O)c(…
|
| ZINC21992198 ZINC | 0.760 | 458.4 Da LogP 2.23 TPSA 197.4 | 2 viol. | Alert |
O=C(O[C@@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(…
|
| ZINC21992201 ZINC | 0.760 | 458.4 Da LogP 2.23 TPSA 197.4 | 2 viol. | Alert |
O=C(O[C@H]1Cc2c(O)cc(O)cc2O[C@H]1c1cc(O)c(O)c(O…
|
| ZINC14813714 ZINC | 0.750 | 300.3 Da LogP 2.59 TPSA 100.1 | ✓ Ro5 | Alert |
COc1cc(O)c2c(=O)cc(-c3ccc(O)c(O)c3)oc2c1
|
| ZINC338283 ZINC | 0.738 | 286.3 Da LogP 2.81 TPSA 76.0 | ✓ Ro5 | ✓ Clean |
COc1cc(O)c2c(c1)O[C@@H](c1ccc(O)cc1)CC2=O
|
| ZINC338284 ZINC | 0.738 | 286.3 Da LogP 2.81 TPSA 76.0 | ✓ Ro5 | ✓ Clean |
COc1cc(O)c2c(c1)O[C@H](c1ccc(O)cc1)CC2=O
|
| ZINC704414 ZINC | 0.736 | 374.2 Da LogP 4.58 TPSA 51.5 | ✓ Ro5 | ✓ Clean |
CCOC(=O)c1c(C)n(-c2ccccc2)c2cc(Br)c(O)cc12
|
| ZINC34764844 ZINC | 0.733 | 206.3 Da LogP 1.09 TPSA 36.9 | ✓ Ro5 | ✓ Clean |
CCCOCCOCCOCCOC
|
| ZINC13520048 ZINC | 0.730 | 302.2 Da LogP 1.99 TPSA 131.4 | ✓ Ro5 | Alert |
O=c1cc(-c2cc(O)c(O)c(O)c2)oc2cc(O)cc(O)c12
|
| ZINC39317 ZINC | 0.730 | 270.2 Da LogP 2.58 TPSA 90.9 | ✓ Ro5 | Alert |
O=c1cc(-c2ccc(O)c(O)c2)oc2cccc(O)c12
|
| ZINC1421880 ZINC | 0.727 | 338.4 Da LogP 3.57 TPSA 54.7 | ✓ Ro5 | ✓ Clean |
CCOC(=O)c1c(CN(C)C)n(-c2ccccc2)c2ccc(O)cc12
|
| ZINC14642643 ZINC | 0.722 | 456.4 Da LogP 2.83 TPSA 166.1 | 1 viol. | Alert |
COc1cc(C(=O)O[C@@H]2Cc3c(O)cc(O)cc3O[C@@H]2c2cc…
|
| ZINC6536308 ZINC | 0.718 | 288.7 Da LogP 3.52 TPSA 70.7 | ✓ Ro5 | ✓ Clean |
O=c1cc(-c2ccc(Cl)cc2)oc2cc(O)cc(O)c12
|
| ZINC14813748 ZINC | 0.714 | 300.3 Da LogP 2.59 TPSA 100.1 | ✓ Ro5 | Alert |
COc1cc(O)cc2oc(-c3ccc(O)c(O)c3)cc(=O)c12
|
| ZINC519621 ZINC | 0.714 | 300.3 Da LogP 2.59 TPSA 100.1 | ✓ Ro5 | ✓ Clean |
COc1cc(-c2cc(=O)c3c(O)cc(O)cc3o2)ccc1O
|
| ZINC5733652 ZINC | 0.714 | 300.3 Da LogP 2.59 TPSA 100.1 | ✓ Ro5 | ✓ Clean |
COc1ccc(-c2cc(=O)c3c(O)cc(O)cc3o2)cc1O
|
| ZINC6041173 ZINC | 0.712 | 443.3 Da LogP 4.87 TPSA 54.7 | ✓ Ro5 | ✓ Clean |
CCOC(=O)c1c(CN2CCCC2)n(-c2ccccc2)c2cc(Br)c(O)cc…
|
| ZINC3872070 ZINC | 0.711 | 254.2 Da LogP 2.87 TPSA 70.7 | ✓ Ro5 | ✓ Clean |
O=c1cc(-c2ccccc2)oc2cc(O)cc(O)c12
|
| ZINC755533 ZINC | 0.704 | 355.2 Da LogP 2.88 TPSA 54.7 | ✓ Ro5 | ✓ Clean |
CCOC(=O)c1c(CN(C)C)n(C)c2cc(Br)c(O)cc12
|
| ZINC14728095 ZINC | 0.700 | 288.3 Da LogP 2.22 TPSA 107.2 | ✓ Ro5 | ✓ Clean |
O=C1C[C@H](c2c(O)cccc2O)Oc2cc(O)cc(O)c21
|
| ZINC6091723 ZINC | 0.700 | 288.3 Da LogP 2.22 TPSA 107.2 | ✓ Ro5 | ✓ Clean |
O=C1C[C@@H](c2c(O)cccc2O)Oc2cc(O)cc(O)c21
|
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.