KpATCC43816 Protein target profile

phosphoglycerate kinase family protein

Accession: VK055_4127

Gene: AIK82673.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H2Q3
Length 382
Pocket druggability (P2Rank · AlphaFold DB model) 0.613
Direct ligand evidence 0 154 total records
Functional annotation 0 EC 2 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on 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 Target 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.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
38.424 Lower values reduce human off-target concern.
Human E-value
9.58e-76
Gut microbiome similarity
6.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
96.335 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
96.54 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.613
Structure A0A0H3H2Q3
Pocket Pocket 1
Druggability (FPocket) 0.876
Structure A0A0H3H2Q3
Pocket Pocket 2
ColabFold model
P2Rank 0.545 · Pocket 1
FPocket 0.374 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 304 / 4744 genomes with a hit
Prevalence 6.4%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MTDLDLAGKRVFIRADLNVPVKDGKVTSDARIRASLPTIELALKQGAKVMVTSHLGRPTEGEYNEEFSLLPVVNYLKDKLSNPVRLVKDYLDGVEVAAGELVVLENVRFNKGEKKDDEELSKKYAALCDVFVMDAFGTAHRAQASTHGIGKFADVACAGPLLAAELDALGKALKEPARPMVAIVGGSKVSTKLTVLDSLSKIADQLIVGGGIANTFVAAQGHNVGKSLYEADLVDEAKRLLGTCDIPVPTDVRVATEFSETATATLKSVNDIKDDEQILDLGDVSAQKLAEILKNAKTILWNGPVGVFEFPNFRKGTEIVANAIADSEGFSIAGGGDTLAAIDLFGIADKISYISTGGGAFLEFVEGKVLPAVAMLEERAKQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

2
  • 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:0004618 Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

36 records
Show feature table
Start End DB Term Name
1 378 SUPERFAMILY SSF53748 Phosphoglycerate kinase
1 378 InterPro IPR036043 Phosphoglycerate kinase superfamily
2 163 FunFam G3DSA:3.40.50.1260:FF:000002 Phosphoglycerate kinase
160 368 Gene3D G3DSA:3.40.50.1260 -
160 368 InterPro IPR015824 Phosphoglycerate kinase, N-terminal
3 378 Hamap MF_00145 Phosphoglycerate kinase [pgk].
3 378 InterPro IPR001576 Phosphoglycerate kinase
164 368 FunFam G3DSA:3.40.50.1260:FF:000001 Phosphoglycerate kinase
181 200 PRINTS PR00477 Phosphoglycerate kinase family signature
181 200 InterPro IPR001576 Phosphoglycerate kinase
26 48 PRINTS PR00477 Phosphoglycerate kinase family signature
26 48 InterPro IPR001576 Phosphoglycerate kinase
158 180 PRINTS PR00477 Phosphoglycerate kinase family signature
158 180 InterPro IPR001576 Phosphoglycerate kinase
127 149 PRINTS PR00477 Phosphoglycerate kinase family signature
127 149 InterPro IPR001576 Phosphoglycerate kinase
298 323 PRINTS PR00477 Phosphoglycerate kinase family signature
298 323 InterPro IPR001576 Phosphoglycerate kinase
331 342 PRINTS PR00477 Phosphoglycerate kinase family signature
331 342 InterPro IPR001576 Phosphoglycerate kinase
99 114 PRINTS PR00477 Phosphoglycerate kinase family signature
99 114 InterPro IPR001576 Phosphoglycerate kinase
5 21 PRINTS PR00477 Phosphoglycerate kinase family signature
5 21 InterPro IPR001576 Phosphoglycerate kinase
354 371 PRINTS PR00477 Phosphoglycerate kinase family signature
354 371 InterPro IPR001576 Phosphoglycerate kinase
1 368 Pfam PF00162 Phosphoglycerate kinase
1 368 InterPro IPR001576 Phosphoglycerate kinase
10 20 ProSitePatterns PS00111 Phosphoglycerate kinase signature.
10 20 InterPro IPR015911 Phosphoglycerate kinase, conserved site
1 382 PIRSF PIRSF000724 Pgk
1 382 InterPro IPR001576 Phosphoglycerate kinase
3 376 Gene3D G3DSA:3.40.50.1260 -
3 376 InterPro IPR015824 Phosphoglycerate kinase, N-terminal
3 379 PANTHER PTHR11406 PHOSPHOGLYCERATE KINASE
3 379 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.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.613
Likely same site as FPocket 2 2.1 Å 15 shared residues 88% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.12
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Surrounding area
Pocket 3 P2Rank #3
0.119
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.069
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.044
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.876 Unusual size
Likely same site as P2Rank 1 2.1 Å 15 shared residues 88% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:113-113
UniProt: Binding site:146-146
UniProt: Binding site:197-197
UniProt: Binding site:21-23
UniProt: Binding site:314-314
UniProt: Binding site:340-343
UniProt: Binding site:36-36
UniProt: Binding site:59-62
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

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 AF_A0A0H3H2Q3
AlphaFold DB full sequence Viewing
ColabFold VK055_4127
ColabFold full sequence Loaded

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 same-protein records
Transferred evidence 104 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3PG PDB via homolog 186.1 Da · LogP -1.46 · TPSA 124.3 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
BIS PDB via homolog Detail RCSB PDB
BTB PDB via homolog Detail RCSB PDB
CHEMBL109037 ChEMBL via homolog Detail ChEMBL

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Chemistry

ChEMBL CHEMBL109037 ChEMBL CHEMBL1160025 ChEMBL CHEMBL1201043 ChEMBL CHEMBL1224512 ChEMBL CHEMBL1257003 ChEMBL CHEMBL1305050 ChEMBL CHEMBL1306943 ChEMBL CHEMBL1310120 ChEMBL CHEMBL1310353 ChEMBL CHEMBL1314571 ChEMBL CHEMBL1317569 ChEMBL CHEMBL1320902 ChEMBL CHEMBL1321572 ChEMBL CHEMBL1325592 ChEMBL CHEMBL1326606 ChEMBL CHEMBL1328733 ChEMBL CHEMBL1329141 ChEMBL CHEMBL1330464 ChEMBL CHEMBL1332402 ChEMBL CHEMBL1337591 ChEMBL CHEMBL1340834 ChEMBL CHEMBL1341816 ChEMBL CHEMBL1346456 ChEMBL CHEMBL1349800 ChEMBL CHEMBL1352624 ChEMBL CHEMBL1353369 ChEMBL CHEMBL1354279 ChEMBL CHEMBL1361920 ChEMBL CHEMBL1362047 ChEMBL CHEMBL1363824 ChEMBL CHEMBL1367248 ChEMBL CHEMBL1371869 ChEMBL CHEMBL1373655 ChEMBL CHEMBL1374603 ChEMBL CHEMBL1375740 ChEMBL CHEMBL1377441 ChEMBL CHEMBL1381590 ChEMBL CHEMBL1383312 ChEMBL CHEMBL1393131 ChEMBL CHEMBL1399010 ChEMBL CHEMBL1399331 ChEMBL CHEMBL1401421 ChEMBL CHEMBL1401747 ChEMBL CHEMBL1402010 ChEMBL CHEMBL1403024 ChEMBL CHEMBL1403191 ChEMBL CHEMBL1403497 ChEMBL CHEMBL1403586 ChEMBL CHEMBL1405834 ChEMBL CHEMBL1406195 ChEMBL CHEMBL1408293 ChEMBL CHEMBL1414730 ChEMBL CHEMBL1415001 ChEMBL CHEMBL1417614 ChEMBL CHEMBL1424694 ChEMBL CHEMBL1427311 ChEMBL CHEMBL1427775 ChEMBL CHEMBL1429479 ChEMBL CHEMBL1430473 ChEMBL CHEMBL1433062 ChEMBL CHEMBL1435178 ChEMBL CHEMBL1439919 ChEMBL CHEMBL1445030 ChEMBL CHEMBL1447877 ChEMBL CHEMBL1448410 ChEMBL CHEMBL1448854 ChEMBL CHEMBL1450797 ChEMBL CHEMBL1452254 ChEMBL CHEMBL1457634 ChEMBL CHEMBL1458130 ChEMBL CHEMBL1459468 ChEMBL CHEMBL1459778 ChEMBL CHEMBL1460470 ChEMBL CHEMBL1477703 ChEMBL CHEMBL1481543 ChEMBL CHEMBL1482590 ChEMBL CHEMBL1486109 ChEMBL CHEMBL1491562 ChEMBL CHEMBL1495778 ChEMBL CHEMBL1498991 ChEMBL CHEMBL1501392 ChEMBL CHEMBL1502860 ChEMBL CHEMBL1505222 ChEMBL CHEMBL1506682 ChEMBL CHEMBL1508847 ChEMBL CHEMBL1510832 ChEMBL CHEMBL1518604 ChEMBL CHEMBL1519965 ChEMBL CHEMBL1522218 ChEMBL CHEMBL1523510 ChEMBL CHEMBL1528737 ChEMBL CHEMBL1536256 ChEMBL CHEMBL1542453 ChEMBL CHEMBL1542762 ChEMBL CHEMBL1546048 ChEMBL CHEMBL1547446 ChEMBL CHEMBL1551368 ChEMBL CHEMBL1555842 ChEMBL CHEMBL1556531 ChEMBL CHEMBL1558192