Protein profile

PA4329

pyruvate kinase

Genome: NC_002516.2

Gene: PA4329 pykA Structure source: Experimental + AlphaFold UniProt Q9HW72
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Amino acids 483
Annotations 10
Features 37
PDB binders 6
Druggability 0.661

Overview

Basic information about this protein and its source genome.

Accession
PA4329
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4329 pykA
Status
annotated
Amino acids
483
Structure source
Experimental + AlphaFold
EC
2.7.1.40
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. 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. GO:0000287 Binding to a magnesium (Mg) ion. GO:0030955 Binding to a potassium ion (K+).

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
56.098
Human E-value
1.48e-08
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 0.661
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MSVRRTKIVATLGPASNSPEVLEQLILAGIDVARLNFSHGTPDEHRARARLVRELAAKHGRFVALLGDLQGPKIRIAKFANKRIELQVGDKFRFSTSHARDAGTQEVVGIDYPDLVKDCGVGDELLLDDGRVVMVVEEVAADELRCRVLIGGPLSDHKGINRRGGGLTAPALTDKDKADIKLAADMDLDYVAVSFPRDAKDMEYARRLLTEAGGKAWLVAKIERAEAVADDDALDGLIRASDAVMVARGDLGVEIGDAELVGIQKKIILHARRNNKVVITATQMMESMIHSPMPTRAEVSDVANAVLDYTDAVMLSAESAAGEYPVEAVKAMARVCQGAEKHPTSQKSSHRLGQTFDRCDESIALASMYTANHFPGIKAIICLTESGFTPLIMSRIRSSVPIYAYSPHRETQARVAMFRGVETIPFDPAALPAEKVSQAAVDELLKRGVVTKGDWVILTKGDSYTAQGGTNTMKVLHVGDLLV

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • 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.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0030955 Binding to a potassium ion (K+).
  • GO:0004743 Catalysis of the reaction: ADP + H+ + phosphoenolpyruvate = ATP + pyruvate.
  • 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: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.

37 records
Show feature table
Start End DB Term Name
4 342 Pfam PF00224 Pyruvate kinase, barrel domain
4 342 InterPro IPR015793 Pyruvate kinase, barrel
361 476 Pfam PF02887 Pyruvate kinase, alpha/beta domain
361 476 InterPro IPR015795 Pyruvate kinase, C-terminal
3 458 PANTHER PTHR11817 PYRUVATE KINASE
3 458 InterPro IPR001697 Pyruvate kinase
72 170 FunFam G3DSA:2.40.33.10:FF:000001 Pyruvate kinase
298 316 PRINTS PR01050 Pyruvate kinase family signature
298 316 InterPro IPR001697 Pyruvate kinase
273 297 PRINTS PR01050 Pyruvate kinase family signature
273 297 InterPro IPR001697 Pyruvate kinase
221 247 PRINTS PR01050 Pyruvate kinase family signature
221 247 InterPro IPR001697 Pyruvate kinase
248 272 PRINTS PR01050 Pyruvate kinase family signature
248 272 InterPro IPR001697 Pyruvate kinase
61 77 PRINTS PR01050 Pyruvate kinase family signature
61 77 InterPro IPR001697 Pyruvate kinase
317 333 PRINTS PR01050 Pyruvate kinase family signature
317 333 InterPro IPR001697 Pyruvate kinase
188 202 PRINTS PR01050 Pyruvate kinase family signature
188 202 InterPro IPR001697 Pyruvate kinase
340 461 Gene3D G3DSA:3.40.1380.20 -
340 461 InterPro IPR036918 Pyruvate kinase, C-terminal domain superfamily
4 339 Gene3D G3DSA:3.20.20.60 -
4 339 InterPro IPR040442 Pyruvate kinase-like domain superfamily
216 228 ProSitePatterns PS00110 Pyruvate kinase active site signature.
216 228 InterPro IPR018209 Pyruvate kinase, active site
72 165 SUPERFAMILY SSF50800 PK beta-barrel domain-like
72 165 InterPro IPR011037 Pyruvate kinase-like, insert domain superfamily
2 343 SUPERFAMILY SSF51621 Phosphoenolpyruvate/pyruvate domain
2 343 InterPro IPR015813 Pyruvate/Phosphoenolpyruvate kinase-like domain superfamily
72 170 Gene3D G3DSA:2.40.33.10 -
72 170 InterPro IPR015806 Pyruvate kinase, insert domain superfamily
4 478 NCBIfam TIGR01064 pyruvate kinase
4 478 InterPro IPR001697 Pyruvate kinase
327 479 SUPERFAMILY SSF52935 PK C-terminal domain-like
327 479 InterPro IPR036918 Pyruvate kinase, C-terminal domain superfamily

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

1 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 6QXL
X-ray 2.43 Å A,B,C,D,E,F,G,H,I,J,K,L
100.0% 1-483
PDBe RCSB PDBj File
Viewing
AlphaFold PA4329
AlphaFold — — 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 0.661
6 0.571

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 14.07 0.71
2 1.98 0.042
3 1.66 0.028
4 1.48 0.02

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.

108 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
3T07
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…
ETE
2G50
P11974 208.3 Da LogP -0.33 TPSA 57.2 ✓ Ro5 ✓ Clean COCCOCCOCCOCCO
OXL
1A49
P11974 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
PEQ
1AQF
P11974 170.1 Da LogP -0.43 TPSA 104.1 ✓ Ro5 ✓ Clean C[C@@H](C(=O)O)OP(=O)(O)O
PYR
1F3W
P11974 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
R5P
6ITO
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

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.