Protein profile

PA5297

pyruvate dehydrogenase

Genome: NC_002516.2

Gene: poxB PA5297 Structure source: AlphaFold UniProt Q9HTQ7
Amino acids 572
Annotations 5
Features 24
PDB binders 17
Druggability 0.876

Overview

Basic information about this protein and its source genome.

Accession
PA5297
Gene
poxB PA5297
Status
annotated
Amino acids
572
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.99
Human E-value
2.32e-07
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
CytoplasmicMembrane

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.

FPocket 0.876
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0052737 Catalysis of the reaction: a ubiquinone + H2O + pyruvate = a ubiquinol + acetate + CO2.
  • GO:0030976 Binding to thiamine pyrophosphate, the diphosphoric ester of thiamine. Acts as a coenzyme of several (de)carboxylases, transketolases, and alpha-oxoacid dehydrogenases.
  • GO:0019752 The chemical reactions and pathways involving carboxylic acids, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
  • 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.

24 records
Show feature table
Start End DB Term Name
177 332 Gene3D G3DSA:3.40.50.1220 -
357 532 CDD cd02014 TPP_POX
357 532 InterPro IPR047212 Pyruvate oxidase POXB-like, PP-binding domain
5 166 CDD cd07039 TPP_PYR_POX
5 166 InterPro IPR047210 Pyruvate oxidase POXB-like, pyrimidine-binding domain
416 435 ProSitePatterns PS00187 Thiamine pyrophosphate enzymes signature.
416 435 InterPro IPR000399 TPP-binding enzyme, conserved site
1 173 Gene3D G3DSA:3.40.50.970 -
458 478 Coils Coil Coil
5 170 Pfam PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
5 170 InterPro IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain
1 570 PANTHER PTHR42981 PYRUVATE DEHYDROGENASE [UBIQUINONE]
1 570 InterPro IPR047211 Pyruvate oxidase/Pyruvate dehydrogenase [ubiquinone]-like
4 182 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
4 182 InterPro IPR029061 Thiamin diphosphate-binding fold
347 572 Gene3D G3DSA:3.40.50.970 -
190 318 Pfam PF00205 Thiamine pyrophosphate enzyme, central domain
190 318 InterPro IPR012000 Thiamine pyrophosphate enzyme, central domain
379 525 Pfam PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
379 525 InterPro IPR011766 Thiamine pyrophosphate enzyme, TPP-binding
181 346 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain
181 346 InterPro IPR029035 DHS-like NAD/FAD-binding domain superfamily
357 558 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
357 558 InterPro IPR029061 Thiamin diphosphate-binding fold

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA5297
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
3 0.876
1 0.6

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.

105 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
1IQ P17597 311.3 Da LogP 2.22 TPSA 91.7 ✓ Ro5 ✓ Clean CC(C)[C@@]1(C(=O)NC(=N1)c2c(cc3ccccc3n2)C(=O)O)C
1MM P17597 381.4 Da LogP 0.49 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1nc(nc(n1)OC)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC
1MS P17597 337.3 Da LogP 1.20 TPSA 144.2 ✓ Ro5 ✓ Clean Cc1ccnc(n1)NC(=O)NS(=O)(=O)c2ccccc2[N+](=O)[O-]
1SM P17597 364.4 Da LogP 1.39 TPSA 127.3 ✓ Ro5 ✓ Clean Cc1cc(nc(n1)NC(=O)NS(=O)(=O)c2ccccc2C(=O)OC)C
6QL P17597 430.4 Da LogP 2.58 TPSA 144.2 1 viol. ✓ Clean COc1cc(nc(n1)Oc2cccc(c2C(=O)O)Oc3nc(cc(n3)OC)OC…
6R4 P17597 398.4 Da LogP 0.10 TPSA 138.6 ✓ Ro5 ✓ Clean CCCOC1=NN(C(=O)N1C)C(=O)NS(=O)(=O)c2ccccc2C(=O)…
6R5 P17597 390.4 Da LogP -0.31 TPSA 138.6 1 viol. ✓ Clean Cc1c(c(cs1)C(=O)OC)S(=O)(=O)NC(=O)N2C(=O)N(C(=N…
F50 P17597 76.1 Da LogP 0.02 TPSA 46.5 ✓ Ro5 ✓ Clean CC(=O)OO
FAB P17597 855.6 Da LogP -2.87 TPSA 373.8 3 viol. Alert Cc1cc2c(cc1C)[N+](=C3C(=O)NC(=O)N=C3N2C[C@@H]([…
HTL P37063 467.4 Da LogP 1.04 TPSA 186.0 ✓ Ro5 ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)C(=O)C)CCO[P@@](=O)(…
P22 P17597 206.0 Da LogP 0.23 TPSA 113.3 ✓ Ro5 ✓ Clean CCO[P@](=O)(O)OP(=O)(O)O
PXD P17597 483.4 Da LogP 2.61 TPSA 116.9 ✓ Ro5 ✓ Clean COc1cnc(n2c1nc(n2)NS(=O)(=O)c3c(cccc3OCC(F)F)C(…
TDK P37063 563.4 Da LogP 0.84 TPSA 235.7 3 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)[P@@](=O)…
TDL P37063 513.4 Da LogP 0.13 TPSA 226.5 2 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](C)(C(=O)O)O)CCO…
TDM P17597 468.4 Da LogP 2.51 TPSA 188.6 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN\2C(=C(S/C2=C(\C)/O)CCO[P@@](=O…
TP9 P17597 412.3 Da LogP -0.03 TPSA 182.8 1 viol. ✓ Clean Cc1ncc(c(n1)N)CN/C(=C(/CCO[P@](=O)([O-])O[P@@](…
TZD P17597 440.3 Da LogP 0.72 TPSA 187.1 ✓ Ro5 ✓ Clean Cc1ncc(c(n1)N)CN2C(=C(SC2=O)CCO[P@@](=O)(O)OP(=…

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.