Protein target profile

PA0552

phosphoglycerate kinase

Genome: NC_002516.2

Gene: PA0552 pgk 3D evidence: AlphaFold DB model UniProt Q9I5Y4
Length 387
Pocket druggability 0.712
Ligand records 154
EC / GO 1 / 6
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

4 signals
How to read this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal TPW pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Overview

Basic information about this protein and its source genome.

Accession
PA0552
Gene
PA0552 pgk
Status
annotated
Amino acids
387
3D evidence
AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
Hit
Human identity (%)
39.709
Human E-value
3.2100000000000002e-86
Gut microbiome off-target
Hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected pocket evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.712
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MTVLKMTDLDLKGKRVLIREDLNVPVKDGQVQSDARIKAALPTLKLALEKGAAVMVCSHLGRPTEGEFSAENSLKPVAEYLSKALGREVPLLADYLDGVEVKAGDLVLFENVRFNKGEKKNADELAQKYAALCDVFVMDAFGTAHRAEGSTHGVARFAKVAAAGPLLAAELDALGKALGNPARPMAAIVAGSKVSTKLDVLNSLAGICDQLIVGGGIANTFLAAAGHKVGKSLYEADLVETAKAIAAKVKVPLPVDVVVAKEFAESAVATVKAIAEVADDDMILDIGPQTAAQFAELLKTSKTILWNGPVGVFEFDQFGEGTRTLANAIADSAAFSIAGGGDTLAAIDKYGIAERISYISTGGGAFLEFVEGKVLPAVEILEQRAKG

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0043531 Binding to ADP, adenosine 5'-diphosphate.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004618 Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H+.
  • GO:0006094 The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records
Show feature table
Start End DB Term Name
6 373 Pfam PF00162 Phosphoglycerate kinase
6 373 InterPro IPR001576 Phosphoglycerate kinase
4 384 PANTHER PTHR11406 PHOSPHOGLYCERATE KINASE
4 384 InterPro IPR001576 Phosphoglycerate kinase
165 373 Gene3D G3DSA:3.40.50.1260 -
165 373 InterPro IPR015824 Phosphoglycerate kinase, N-terminal
15 25 ProSitePatterns PS00111 Phosphoglycerate kinase signature.
15 25 InterPro IPR015911 Phosphoglycerate kinase, conserved site
31 53 PRINTS PR00477 Phosphoglycerate kinase family signature
31 53 InterPro IPR001576 Phosphoglycerate kinase
132 154 PRINTS PR00477 Phosphoglycerate kinase family signature
132 154 InterPro IPR001576 Phosphoglycerate kinase
336 347 PRINTS PR00477 Phosphoglycerate kinase family signature
336 347 InterPro IPR001576 Phosphoglycerate kinase
186 205 PRINTS PR00477 Phosphoglycerate kinase family signature
186 205 InterPro IPR001576 Phosphoglycerate kinase
104 119 PRINTS PR00477 Phosphoglycerate kinase family signature
104 119 InterPro IPR001576 Phosphoglycerate kinase
10 26 PRINTS PR00477 Phosphoglycerate kinase family signature
10 26 InterPro IPR001576 Phosphoglycerate kinase
359 376 PRINTS PR00477 Phosphoglycerate kinase family signature
359 376 InterPro IPR001576 Phosphoglycerate kinase
163 185 PRINTS PR00477 Phosphoglycerate kinase family signature
163 185 InterPro IPR001576 Phosphoglycerate kinase
303 328 PRINTS PR00477 Phosphoglycerate kinase family signature
303 328 InterPro IPR001576 Phosphoglycerate kinase
8 383 Hamap MF_00145 Phosphoglycerate kinase [pgk].
8 383 InterPro IPR001576 Phosphoglycerate kinase
7 168 FunFam G3DSA:3.40.50.1260:FF:000002 Phosphoglycerate kinase
8 381 Gene3D G3DSA:3.40.50.1260 -
8 381 InterPro IPR015824 Phosphoglycerate kinase, N-terminal
169 373 FunFam G3DSA:3.40.50.1260:FF:000001 Phosphoglycerate kinase
4 383 SUPERFAMILY SSF53748 Phosphoglycerate kinase
4 383 InterPro IPR036043 Phosphoglycerate kinase superfamily
1 387 PIRSF PIRSF000724 Pgk
1 387 InterPro IPR001576 Phosphoglycerate kinase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

3D visualization script Full viewer

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Structural evidence

0 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB PA0552
AlphaFold DB full sequence Viewing
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1
0.712
Show in viewer
Site 2 FPocket #2
0.513
Show in viewer
Site 3 FPocket #4
0.257
Show in viewer

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.

154 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 154 via homologs
Structural ligands 4 0 loaded crystals
Bioactive compounds 100 50 ZINC proposed compounds
Drug-like & clean 86 59 PAINS alerts
Best available ligand signal
3PG PDB via homolog 186.1 Da · LogP -1.46 · TPSA 124.3 Open detail RCSB PDB
Detail RCSB PDB 3PG PDB via homolog
Detail RCSB PDB ANP PDB via homolog
Detail RCSB PDB BIS PDB via homolog
Detail RCSB PDB BTB PDB via homolog

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
3PG RCSB PDB P07378 186.1 Da LogP -1.46 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)OP(=O)(O)O
ANP RCSB PDB P36204 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BIS RCSB PDB P07378 633.3 Da LogP 0.88 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BTB RCSB PDB Q81X75 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO

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.