Protein profile

KP13_01880

Pyruvate dehydrogenase E1 component

Genome: KpKP13

Gene: AHE46320.1 aceE Structure source: AlphaFold + ColabFold UniProt A0A0H3GMN6
Amino acids 887
Annotations 5
Features 24
PDB binders 12
Druggability 0.731

Overview

Basic information about this protein and its source genome.

Accession
KP13_01880
Gene
AHE46320.1 aceE
Status
annotated
Amino acids
887
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.756
Human E-value
7.35e-09
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
95.152
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.65

Selected Druggability evidence

AlphaFold / UniProt model

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 0.731
Structure A0A0H3GMN6
Pocket Pocket 5
P2Rank 0.404
Structure A0A0H3GMN6
Pocket Pocket 1
ColabFold model
FPocket 0.899 · Pocket 51
P2Rank 0.707 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 261 / 4744 genomes with a hit
Normalized 0.055

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

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: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:0000287 Binding to a magnesium (Mg) ion.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
488 700 Pfam PF17831 Pyruvate dehydrogenase E1 component middle domain
488 700 InterPro IPR041621 Pyruvate dehydrogenase E1 component, middle domain
133 294 Pfam PF00456 Transketolase, thiamine diphosphate binding domain
133 294 InterPro IPR005474 Transketolase, N-terminal
472 706 FunFam G3DSA:3.40.50.970:FF:000009 Pyruvate dehydrogenase E1 component
472 706 Gene3D G3DSA:3.40.50.970 -
1 887 PIRSF PIRSF000156 Pyruvate_dh_E1
1 887 InterPro IPR004660 Pyruvate dehydrogenase E1 component
59 469 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
59 469 InterPro IPR029061 Thiamin diphosphate-binding fold
474 701 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
474 701 InterPro IPR029061 Thiamin diphosphate-binding fold
5 886 NCBIfam TIGR00759 pyruvate dehydrogenase (acetyl-transferring), homodimeric type
5 886 InterPro IPR004660 Pyruvate dehydrogenase E1 component
702 885 SUPERFAMILY SSF52922 TK C-terminal domain-like
702 885 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
707 887 Gene3D G3DSA:3.40.50.920 -
707 887 InterPro IPR009014 Transketolase C-terminal/Pyruvate-ferredoxin oxidoreductase domain II
57 471 FunFam G3DSA:3.40.50.970:FF:000011 Pyruvate dehydrogenase E1 component
76 461 CDD cd02017 TPP_E1_EcPDC_like
76 461 InterPro IPR035807 Pyruvate dehydrogenase E1 component, N-terminal
58 471 Gene3D G3DSA:3.40.50.970 -
67 861 PANTHER PTHR43825 PYRUVATE DEHYDROGENASE E1 COMPONENT
707 887 FunFam G3DSA:3.40.50.920:FF:000005 Pyruvate dehydrogenase E1 component

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 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GMN6
AlphaFold full sequence Viewing
ColabFold KP13_01880
ColabFold full sequence Loaded
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
5 0.731
1 0.391

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 8.18 0.436
2 5.95 0.292
3 3.26 0.113
4 2.97 0.096
5 1.93 0.04

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.

90 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…
5SP P27302 230.1 Da LogP -2.62 TPSA 144.5 ✓ Ro5 ✓ Clean C([C@H]([C@@H](C(=O)CO)O)O)OP(=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
NDQ P27302 441.3 Da LogP 0.54 TPSA 178.2 ✓ Ro5 ✓ Clean Cc1c(sc[n+]1Cc2cnc(nc2N)OC)CCOP(=O)(O)OP(=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)…
T5X P27302 655.4 Da LogP -2.15 TPSA 316.6 3 viol. ✓ Clean Cc1c(sc([n+]1Cc2cnc(nc2N)C)[C@](CO)([C@H]([C@@H…
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)…
TZD P0AFG8 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.