Protein profile

KP13_04234

Pyruvate dehydrogenase ubiquinone

Genome: KpKP13

Gene: poxB AHE45465.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUU8
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Amino acids 575
Annotations 11
Features 28
PDB binders 17
Druggability 0.814

Overview

Basic information about this protein and its source genome.

Accession
KP13_04234
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
poxB AHE45465.1
Status
annotated
Amino acids
575
Structure source
AlphaFold + ColabFold
EC
1.2.5.1
GO
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:0052737 Catalysis of the reaction: a ubiquinone + H2O + pyruvate = a ubiquinol + acetate + CO2. GO:0000287 Binding to a magnesium (Mg) ion. 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:0006090 The chemical reactions and pathways involving pyruvate, 2-oxopropanoate. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
31.0
Human E-value
1.9e-06
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
CytoplasmicMembrane
ColabFold pLDDT
94.1

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 0.814
Structure A0A0H3GUU8
Pocket Pocket 2
P2Rank 0.79
Structure A0A0H3GUU8
Pocket Pocket 1
ColabFold model
FPocket 0.793 · Pocket 21
P2Rank 0.747 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 138 / 4744 genomes with a hit
Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • 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:0052737 Catalysis of the reaction: a ubiquinone + H2O + pyruvate = a ubiquinol + acetate + CO2.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • 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:0006090 The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
  • GO:0008289 Binding to a lipid.
  • GO:0048039 Binding to ubiquinone, a quinone derivative with a tail of isoprene units.
  • GO:0042867 The chemical reactions and pathways resulting in the breakdown of pyruvate, 2-oxopropanoate.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
7 169 CDD cd07039 TPP_PYR_POX
7 169 InterPro IPR047210 Pyruvate oxidase POXB-like, pyrimidine-binding domain
185 355 SUPERFAMILY SSF52467 DHS-like NAD/FAD-binding domain
185 355 InterPro IPR029035 DHS-like NAD/FAD-binding domain superfamily
360 536 CDD cd02014 TPP_POX
360 536 InterPro IPR047212 Pyruvate oxidase POXB-like, PP-binding domain
7 173 Pfam PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain
7 173 InterPro IPR012001 Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain
4 179 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
4 179 InterPro IPR029061 Thiamin diphosphate-binding fold
419 438 ProSitePatterns PS00187 Thiamine pyrophosphate enzymes signature.
419 438 InterPro IPR000399 TPP-binding enzyme, conserved site
5 575 Hamap MF_00850 Pyruvate dehydrogenase [ubiquinone] [poxB].
5 575 InterPro IPR044261 Pyruvate dehydrogenase [ubiquinone]
348 575 FunFam G3DSA:3.40.50.970:FF:000031 Pyruvate dehydrogenase [ubiquinone]
348 575 Gene3D G3DSA:3.40.50.970 -
4 181 FunFam G3DSA:3.40.50.970:FF:000025 Ubiquinone-dependent pyruvate dehydrogenase
195 322 Pfam PF00205 Thiamine pyrophosphate enzyme, central domain
195 322 InterPro IPR012000 Thiamine pyrophosphate enzyme, central domain
4 574 PANTHER PTHR42981 PYRUVATE DEHYDROGENASE [UBIQUINONE]
4 574 InterPro IPR047211 Pyruvate oxidase/Pyruvate dehydrogenase [ubiquinone]-like
182 336 Gene3D G3DSA:3.40.50.1220 -
182 336 FunFam G3DSA:3.40.50.1220:FF:000013 Pyruvate dehydrogenase [ubiquinone]
4 181 Gene3D G3DSA:3.40.50.970 -
360 560 SUPERFAMILY SSF52518 Thiamin diphosphate-binding fold (THDP-binding)
360 560 InterPro IPR029061 Thiamin diphosphate-binding fold
382 528 Pfam PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain
382 528 InterPro IPR011766 Thiamine pyrophosphate enzyme, TPP-binding

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_A0A0H3GUU8
AlphaFold — — full sequence — Viewing
ColabFold KP13_04234
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
2 0.814

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 15.65 0.758
2 6.52 0.33
3 5.46 0.26
4 4.42 0.187
5 2.77 0.084

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
1Z8N
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
1YHY
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
3E9Y
P17597 337.3 Da LogP 1.20 TPSA 144.2 ✓ Ro5 ✓ Clean Cc1ccnc(n1)NC(=O)NS(=O)(=O)c2ccccc2[N+](=O)[O-]
1SM
1YI0
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
5K3S
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
5K6T
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
5K6R
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
5WJ1
P17597 76.1 Da LogP 0.02 TPSA 46.5 ✓ Ro5 ✓ Clean CC(=O)OO
FAB
3E9Y
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
2EZU
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
1YBH
P17597 206.0 Da LogP 0.23 TPSA 113.3 ✓ Ro5 ✓ Clean CCO[P@](=O)(O)OP(=O)(O)O
PXD
5WJ1
P17597 483.4 Da LogP 2.61 TPSA 116.9 ✓ Ro5 ✓ Clean COc1cnc(n2c1nc(n2)NS(=O)(=O)c3c(cccc3OCC(F)F)C(…
TDK
2EZ9
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
2EZ8
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
3E9Y
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
5K2O
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
5K6T
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.