Protein profile

VK055_0078

pyruvate kinase

Genome: KpATCC43816

Gene: AIK78706.1 pyk Structure source: AlphaFold + ColabFold UniProt A0A0H3GRZ9
Amino acids 480
Annotations 8
Features 40
PDB binders 10
Druggability 0.537

Overview

Basic information about this protein and its source genome.

Accession
VK055_0078
Gene
AIK78706.1 pyk
Status
annotated
Amino acids
480
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
50.0
Human E-value
5.61e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
76.875
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.37

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 0.537
Structure A0A0H3GRZ9
Pocket Pocket 18
P2Rank 0.828
Structure A0A0H3GRZ9
Pocket Pocket 1
ColabFold model
FPocket 0.516 · Pocket 12
P2Rank 0.662 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 179 / 4744 genomes with a hit
Normalized 0.038

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0030955 Binding to a potassium ion (K+).
  • GO:0004743 Catalysis of the reaction: ADP + H+ + phosphoenolpyruvate = ATP + pyruvate.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

40 records
Show feature table
Start End DB Term Name
218 230 ProSitePatterns PS00110 Pyruvate kinase active site signature.
218 230 InterPro IPR018209 Pyruvate kinase, active site
3 459 PANTHER PTHR11817 PYRUVATE KINASE
3 459 InterPro IPR001697 Pyruvate kinase
329 479 SUPERFAMILY SSF52935 PK C-terminal domain-like
329 479 InterPro IPR036918 Pyruvate kinase, C-terminal domain superfamily
345 478 FunFam G3DSA:3.40.1380.20:FF:000004 Pyruvate kinase
8 338 Gene3D G3DSA:3.20.20.60 -
8 338 InterPro IPR040442 Pyruvate kinase-like domain superfamily
363 477 Pfam PF02887 Pyruvate kinase, alpha/beta domain
363 477 InterPro IPR015795 Pyruvate kinase, C-terminal
341 478 Gene3D G3DSA:3.40.1380.20 -
341 478 InterPro IPR036918 Pyruvate kinase, C-terminal domain superfamily
6 344 Pfam PF00224 Pyruvate kinase, barrel domain
6 344 InterPro IPR015793 Pyruvate kinase, barrel
4 344 SUPERFAMILY SSF51621 Phosphoenolpyruvate/pyruvate domain
4 344 InterPro IPR015813 Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
75 171 FunFam G3DSA:2.40.33.10:FF:000002 Pyruvate kinase
74 168 SUPERFAMILY SSF50800 PK beta-barrel domain-like
74 168 InterPro IPR011037 Pyruvate kinase-like, insert domain superfamily
5 479 CDD cd00288 Pyruvate_Kinase
5 479 InterPro IPR001697 Pyruvate kinase
75 171 Gene3D G3DSA:2.40.33.10 -
75 171 InterPro IPR015806 Pyruvate kinase, insert domain superfamily
300 318 PRINTS PR01050 Pyruvate kinase family signature
300 318 InterPro IPR001697 Pyruvate kinase
319 335 PRINTS PR01050 Pyruvate kinase family signature
319 335 InterPro IPR001697 Pyruvate kinase
223 249 PRINTS PR01050 Pyruvate kinase family signature
223 249 InterPro IPR001697 Pyruvate kinase
275 299 PRINTS PR01050 Pyruvate kinase family signature
275 299 InterPro IPR001697 Pyruvate kinase
63 79 PRINTS PR01050 Pyruvate kinase family signature
63 79 InterPro IPR001697 Pyruvate kinase
250 274 PRINTS PR01050 Pyruvate kinase family signature
250 274 InterPro IPR001697 Pyruvate kinase
190 204 PRINTS PR01050 Pyruvate kinase family signature
190 204 InterPro IPR001697 Pyruvate kinase
6 479 NCBIfam TIGR01064 pyruvate kinase
6 479 InterPro IPR001697 Pyruvate kinase

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_A0A0H3GRZ9
AlphaFold full sequence Viewing
ColabFold VK055_0078
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
18 0.537

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 13.35 0.683
2 3.29 0.115
3 3.19 0.109

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.

114 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
09C Q6GG09 488.2 Da LogP 4.68 TPSA 72.7 ✓ Ro5 ✓ Clean c1cc2c(cc1Br)[nH]cc2[C@H]3C(=O)NCC(N3)c4c[nH]c5…
LSA Q27686 183.2 Da LogP 0.12 TPSA 63.2 ✓ Ro5 ✓ Clean c1ccc2c(c1)C(=O)NS2(=O)=O
OXL P9WKE5 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
PTK Q27686 522.5 Da LogP 1.57 TPSA 217.5 1 viol. ✓ Clean c1cc2c(cc(c3c2c4c1c(cc(c4cc3)S(=O)(=O)O)S(=O)(=…
QV6 Q27686 620.7 Da LogP 5.98 TPSA 166.9 2 viol. Alert Cc1cc(c(cc1Nc2ccc(c3c2C(=O)c4ccccc4C3=O)Nc5c(cc…
QV7 Q27686 672.7 Da LogP 4.36 TPSA 287.1 2 viol. Alert c1cc(ccc1/N=N/c2ccc(c(c2)S(=O)(=O)O)/N=N/c3c4cc…
QV8 Q27686 379.4 Da LogP 3.45 TPSA 100.5 ✓ Ro5 Alert c1ccc(cc1)Nc2cc(cc3c2C(=O)c4ccccc4C3=O)S(=O)(=O…
R5P P9WKE5 230.1 Da LogP -2.62 TPSA 144.5 ✓ Ro5 ✓ Clean C(C(C(C(C=O)O)O)O)OP(=O)(O)O
S62 Q27686 295.3 Da LogP 0.79 TPSA 121.6 ✓ Ro5 ✓ Clean c1cc2c(cc1S(=O)(=O)O)nc(s2)S(=O)(=O)O
SVR Q27686 1297.3 Da LogP 6.74 TPSA 483.7 4 viol. ✓ Clean Cc1ccc(cc1NC(=O)c2cccc(c2)NC(=O)Nc3cccc(c3)C(=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.