Protein profile
PA3416
pyruvate dehydrogenase E1 component subunit beta
Genome: NC_002516.2
Overview
Basic information about this protein and its source genome.
- Accession
- PA3416
- Gene
- PA3416
- Status
- annotated
- Amino acids
- 333
- Structure source
- AlphaFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 40.122
- Human E-value
- 2.99e-85
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- Localization
- Unknown
Selected Druggability evidence
Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
4- 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:0009083 The chemical reactions and pathways resulting in the breakdown of amino acids containing a branched carbon skeleton, comprising isoleucine, leucine and valine.
- GO:0007584 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a nutrient stimulus.
- GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 205 | 332 | Gene3D | G3DSA:3.40.50.920 | - |
| 205 | 332 | InterPro | IPR009014 | Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II |
| 3 | 330 | PANTHER | PTHR42980 | 2-OXOISOVALERATE DEHYDROGENASE SUBUNIT BETA-RELATED |
| 11 | 186 | SMART | SM00861 | Transket_pyr_3 |
| 11 | 186 | InterPro | IPR005475 | Transketolase-like, pyrimidine-binding domain |
| 12 | 186 | Pfam | PF02779 | Transketolase, pyrimidine binding domain |
| 12 | 186 | InterPro | IPR005475 | Transketolase-like, pyrimidine-binding domain |
| 205 | 322 | Pfam | PF02780 | Transketolase, C-terminal domain |
| 205 | 322 | InterPro | IPR033248 | Transketolase, C-terminal domain |
| 11 | 195 | SUPERFAMILY | SSF52518 | Thiamin diphosphate-binding fold (THDP-binding) |
| 11 | 195 | InterPro | IPR029061 | Thiamin diphosphate-binding fold |
| 8 | 200 | Gene3D | G3DSA:3.40.50.970 | - |
| 197 | 331 | SUPERFAMILY | SSF52922 | TK C-terminal domain-like |
| 197 | 331 | InterPro | IPR009014 | Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II |
| 8 | 199 | FunFam | G3DSA:3.40.50.970:FF:000001 | Pyruvate dehydrogenase E1 beta subunit |
| 200 | 331 | FunFam | G3DSA:3.40.50.920:FF:000001 | Pyruvate dehydrogenase E1 beta subunit |
| 15 | 181 | CDD | cd07036 | TPP_PYR_E1-PDHc-beta_like |
3D Structure
Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.
Loading 3D structure...
Structural evidence
0 + 1Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
PA3416
|
AlphaFold | — | — | full sequence | — | Viewing |
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer
Pockets (FPOCKET)
Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).
| FPOCKET | Sticks | Spheres | Surfaces | Druggability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|
| 1 | 0.333 | ||||||
| 8 | 0.25 |
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.
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 |
|---|---|---|---|---|---|---|
| 4MV | Q5SLR3 | 116.2 Da LogP 1.51 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CC(C)CCC(=O)O
|
|
| A5X | P11177 | 533.4 Da LogP 0.47 TPSA 226.5 | 2 viol. | ✓ Clean |
Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)P(=O)O)CC…
|
|
| COI | P09061 | 130.1 Da LogP 0.69 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CC(C)CC(=O)C(=O)O
|
|
| PYR | P21874 | 88.1 Da LogP -0.34 TPSA 54.4 | ✓ Ro5 | ✓ Clean |
CC(=O)C(=O)O
|
|
| THV | P21953 | 496.4 Da LogP 1.75 TPSA 189.2 | ✓ Ro5 | ✓ Clean |
Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](C(C)C)O)CCO[P@@…
|
|
| THW | P21953 | 530.4 Da LogP 2.14 TPSA 189.2 | 1 viol. | ✓ Clean |
Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C-](c3ccccc3)O)CCO[…
|
|
| THY | P21953 | 510.4 Da LogP 2.14 TPSA 189.2 | 1 viol. | ✓ Clean |
CC[C@H](C)[C-](c1[n+](c(c(s1)CCO[P@](=O)(O)OP(=…
|
|
| TZD | P21953 | 440.3 Da LogP 0.72 TPSA 187.1 | ✓ Ro5 | ✓ Clean |
Cc1ncc(c(n1)N)CN2C(=C(SC2=O)CCO[P@@](=O)(O)OP(=…
|
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 |
|---|---|---|---|---|---|
| ZINC1841074 | 0.636 | 200.3 Da LogP 3.85 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CC(C)CCCCCCCCC(=O)O
|
| ZINC2013445 | 0.636 | 214.3 Da LogP 4.24 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CC(C)CCCCCCCCCC(=O)O
|
| ZINC2575042 | 0.636 | 228.4 Da LogP 4.63 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CC(C)CCCCCCCCCCC(=O)O
|
| ZINC8215517 | 0.618 | 425.3 Da LogP 0.84 TPSA 169.0 | ✓ Ro5 | ✓ Clean |
Cc1ncc(C[n+]2csc(CCO[P@@](=O)(O)OP(=O)(O)O)c2C)…
|
| ZINC145838685 | 0.583 | 200.3 Da LogP 3.70 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CC(C)CCC[C@@H](C)CCCC(=O)O
|
| ZINC145838882 | 0.583 | 200.3 Da LogP 3.70 TPSA 37.3 | ✓ Ro5 | ✓ Clean |
CC(C)CCC[C@H](C)CCCC(=O)O
|
| ZINC13540298 | 0.556 | 440.3 Da LogP 0.72 TPSA 187.1 | ✓ Ro5 | ✓ Clean |
Cc1ncc(Cn2c(C)c(CCO[P@@](=O)(O)OP(=O)(O)O)sc2=O…
|
| ZINC2492519 | 0.542 | 201.3 Da LogP 2.08 TPSA 40.5 | ✓ Ro5 | ✓ Clean |
CC(C)CN(CCC(=O)O)CC(C)C
|
| ZINC1532839 | 0.529 | 345.3 Da LogP 0.72 TPSA 122.4 | ✓ Ro5 | ✓ Clean |
Cc1ncc(C[n+]2csc(CCOP(=O)(O)O)c2C)c(N)n1
|
| ZINC13520374 | 0.528 | 426.3 Da LogP 0.97 TPSA 163.2 | ✓ Ro5 | ✓ Clean |
Cc1ncc(C[n+]2csc(CCO[P@@](=O)(O)OP(=O)(O)O)c2C)…
|
| ZINC1690029 | 0.524 | 204.2 Da LogP 0.42 TPSA 111.9 | ✓ Ro5 | ✓ Clean |
O=C(O)CCC(CCC(=O)O)C(=O)O
|
| ZINC96509633 | 0.522 | 228.2 Da LogP 1.89 TPSA 74.6 | ✓ Ro5 | ✓ Clean |
O=C(O)CCC(CCC(=O)O)C(F)(F)F
|
| ZINC4784097 | 0.500 | 201.3 Da LogP 1.40 TPSA 66.4 | ✓ Ro5 | ✓ Clean |
CC(C)CCNC(=O)CCCC(=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.