Protein profile

PA5015

pyruvate dehydrogenase subunit E1

Genome: NC_002516.2

Gene: PA5015 aceE aceA Structure source: AlphaFold UniProt Q59637
Amino acids 882
Annotations 4
Features 22
PDB binders 8
Druggability 0.747

Overview

Basic information about this protein and its source genome.

Accession
PA5015
Gene
PA5015 aceE aceA
Status
annotated
Amino acids
882
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.539
Human E-value
2.82e-09
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

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 0.747
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MQDLDPVETQEWLDALESVLDREGEDRAHYLMTRMGELASRSGTQLPYAITTPYRNTIPVTHEARMPGDLFMERRIRSLVRWNALAMVMRANKHDPDLGGHISTFASSATLYDIGFNYFFQAPTDEHGGDLVFFQGHASPGVYARAFLEGRISEEQLENFRQEVDGNGLSSYPHPWLMPDFWQFPTVSMGLGPIQAIYQARFMKYLESRGFIPAGKQKVWCFMGDGECDEPESLGAISLAGREKLDNLIFVINCNLQRLDGPVRGNAKIIQELEGVFRGAEWNVNKVIWGRFWDPLFAKDTAGLLQQRMDEVIDGEYQNYKAKDGAYVREHFFGARPELLEMVKDLSDEEIWKLNRGGHDPYKVYAAYHQAVNHKGQPTVILAKTIKGYGTGSGEAKNIAHNVKKVDVDSLRAFRDKFDIPVKDADLEKLPFYKPEEGSAEAKYLAERRAALGGFMPVRRQKSMSVPVPPLETLKAMLDGSGDREISTTMAFVRIISQLVKDKELGPRIVPIVPDEARTFGMEGMFRQLGIYSSVGQLYEPVDKDQVMFYREDKKGQILEEGINEAGAMSSWIAAGTSYSTHNQPMLPFYIFYSMFGFQRIGDLAWAAGDSRAHGFLIGGTAGRTTLNGEGLQHEDGHSHLLASTIPNCRTYDPTYAYELAVIIREGSRQMIEEQQDIFYYITVMNENYVQPAMPKGAEEGIIKGMYLLEEDKKEAAHHVQLLGSGTILREVEEAAKLLRNDFGIGADVWSVPSFNELRRDGLAVERWNRLHPGQKPKQSYVEECLGGRRGPVIASTDYMKLYAEQIRQWVPSKEYKVLGTDGFGRSDSRKKLRNFFEVDRHWVVLAALEALADRGDIEPKVVAEAIAKYGIDPEKRNPLDC

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0004739 Catalysis of the reaction: N(6)-[(R)-lipoyl]-L-lysyl-[protein] + pyruvate + H+ = N(6)-[(R)-S(8)-acetyldihydrolipoyl]-L-lysyl-[protein] + CO2.
  • 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.
  • 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.

22 records
Show feature table
Start End DB Term Name
123 287 Pfam PF00456 Transketolase, thiamine diphosphate binding domain
123 287 InterPro IPR005474 Transketolase, N-terminal
2 880 NCBIfam TIGR00759 pyruvate dehydrogenase (acetyl-transferring), homodimeric type
2 880 InterPro IPR004660 Pyruvate dehydrogenase E1 component
694 880 SUPERFAMILY SSF52922 TK C-terminal domain-like
694 880 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
51 464 Gene3D G3DSA:3.40.50.970 -
1 882 PIRSF PIRSF000156 Pyruvate_dh_E1
1 882 InterPro IPR004660 Pyruvate dehydrogenase E1 component
51 464 FunFam G3DSA:3.40.50.970:FF:000011 Pyruvate dehydrogenase E1 component
699 881 Gene3D G3DSA:3.40.50.920 -
699 881 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
465 698 Gene3D G3DSA:3.40.50.970 -
52 460 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
52 460 InterPro IPR029061 Thiamin diphosphate-binding fold
62 856 PANTHER PTHR43825 PYRUVATE DEHYDROGENASE E1 COMPONENT
473 692 Pfam PF17831 Pyruvate dehydrogenase E1 component middle domain
473 692 InterPro IPR041621 Pyruvate dehydrogenase E1 component, middle domain
70 454 CDD cd02017 TPP_E1_EcPDC_like
70 454 InterPro IPR035807 Pyruvate dehydrogenase E1 component, N-terminal
466 693 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
466 693 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.

3D visualization script Full viewer

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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 PA5015
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 0.747
26 0.395
7 0.348

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.

87 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
1U0 P29401 483.4 Da LogP 1.12 TPSA 205.5 1 viol. ✓ Clean Cc1c(sc(c1Cc2cnc(nc2N)C)[C@@H](CO)O)CCOP(=O)(O)…
1Y7 P29401 292.2 Da LogP -4.11 TPSA 188.1 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H]([C@@H]([C@@H](COP(=O)(O)O…
DX5 P29401 232.1 Da LogP -2.83 TPSA 147.7 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H](COP(=O)(O)O)O)O)O)O
R5P Q0P7Y3 230.1 Da LogP -2.62 TPSA 144.5 ✓ Ro5 ✓ Clean C(C(C(C(C=O)O)O)O)OP(=O)(O)O
RP5 Q0P7Y3 230.1 Da LogP -2.47 TPSA 136.7 ✓ Ro5 ✓ Clean C([C@@H]1[C@H]([C@H]([C@@H](O1)O)O)O)OP(=O)(O)O
S6P P29401 262.2 Da LogP -3.47 TPSA 167.9 1 viol. ✓ Clean C([C@@H]([C@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O)…
T6F P29401 685.5 Da LogP -2.79 TPSA 336.9 3 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](CO)([C@H]([C@@H…
TDK P0AFG8 563.4 Da LogP 0.84 TPSA 235.7 3 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@@](C)(O)[P@@](=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.