Protein target profile

KP13_02160

Phosphoglycerate kinase

Genome: KpKP13 Gene: AHE42732.1 pgk 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H2Q3
Length 387
Pocket druggability 0.876
Direct ligand evidence 0 153 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 (%)
37.956 Lower values reduce human off-target concern.
Human E-value
6.909999999999998e-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 (%)
96.382 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.49 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.876
Structure A0A0H3H2Q3
Pocket Pocket 2
P2Rank 0.613
Structure A0A0H3H2Q3
Pocket Pocket 1
ColabFold model
FPocket 0.51 · Pocket 1
P2Rank 0.696 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 304 / 4744 genomes with a hit
Prevalence 6.4%

Cross-references

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

Chemistry

ChEMBL C04 ChEMBL CHEMBL119171 ChEMBL CHEMBL125044 ChEMBL CHEMBL1257003 ChEMBL CHEMBL1271266 ChEMBL CHEMBL1301673 ChEMBL CHEMBL1302758 ChEMBL CHEMBL1303948 ChEMBL CHEMBL1305050 ChEMBL CHEMBL1305393 ChEMBL CHEMBL1305422 ChEMBL CHEMBL1306943 ChEMBL CHEMBL1310120 ChEMBL CHEMBL1310309 ChEMBL CHEMBL1310353 ChEMBL CHEMBL1312353 ChEMBL CHEMBL1313891 ChEMBL CHEMBL1315592 ChEMBL CHEMBL1315784 ChEMBL CHEMBL1317569 ChEMBL CHEMBL1318358 ChEMBL CHEMBL1319645 ChEMBL CHEMBL1320230 ChEMBL CHEMBL1320799 ChEMBL CHEMBL1321993 ChEMBL CHEMBL1323674 ChEMBL CHEMBL1325592 ChEMBL CHEMBL1325945 ChEMBL CHEMBL1326833 ChEMBL CHEMBL1328733 ChEMBL CHEMBL1330058 ChEMBL CHEMBL1332402 ChEMBL CHEMBL1333760 ChEMBL CHEMBL133576 ChEMBL CHEMBL1340834 ChEMBL CHEMBL1341816 ChEMBL CHEMBL1342038 ChEMBL CHEMBL1342147 ChEMBL CHEMBL1344399 ChEMBL CHEMBL1346055 ChEMBL CHEMBL1346456 ChEMBL CHEMBL1346592 ChEMBL CHEMBL1352624 ChEMBL CHEMBL1354721 ChEMBL CHEMBL1356785 ChEMBL CHEMBL1357911 ChEMBL CHEMBL1358338 ChEMBL CHEMBL1358848 ChEMBL CHEMBL1359859 ChEMBL CHEMBL1360321 ChEMBL CHEMBL1361920 ChEMBL CHEMBL1362047 ChEMBL CHEMBL1362526 ChEMBL CHEMBL1362935 ChEMBL CHEMBL1363706 ChEMBL CHEMBL1365058 ChEMBL CHEMBL1366175 ChEMBL CHEMBL1366347 ChEMBL CHEMBL1366942 ChEMBL CHEMBL1367248 ChEMBL CHEMBL1368108 ChEMBL CHEMBL1370165 ChEMBL CHEMBL1370873 ChEMBL CHEMBL1371301 ChEMBL CHEMBL1373210 ChEMBL CHEMBL1373655 ChEMBL CHEMBL1374603 ChEMBL CHEMBL1375740 ChEMBL CHEMBL1376754 ChEMBL CHEMBL1377441 ChEMBL CHEMBL1377900 ChEMBL CHEMBL1381017 ChEMBL CHEMBL1381590 ChEMBL CHEMBL1381627 ChEMBL CHEMBL1383078 ChEMBL CHEMBL1383244 ChEMBL CHEMBL1383312 ChEMBL CHEMBL1383849 ChEMBL CHEMBL1385494 ChEMBL CHEMBL1386322 ChEMBL CHEMBL1386802 ChEMBL CHEMBL1387610 ChEMBL CHEMBL1387693 ChEMBL CHEMBL1389163 ChEMBL CHEMBL1389177 ChEMBL CHEMBL1390512 ChEMBL CHEMBL1390868 ChEMBL CHEMBL1391256 ChEMBL CHEMBL1391547 ChEMBL CHEMBL1392570 ChEMBL CHEMBL1394649 ChEMBL CHEMBL1395404 ChEMBL CHEMBL1397359 ChEMBL CHEMBL1397687 ChEMBL CHEMBL1397916 ChEMBL CHEMBL1398964 ChEMBL CHEMBL1399010 ChEMBL CHEMBL1402010 ChEMBL CHEMBL1403024 ChEMBL CHEMBL1514259

Sequence

Primary amino-acid sequence viewer.

MSVIKMTDLDLAGKRVFIRADLNVPVKDGKVTSDARIRASLPTIELALKQGAKVMVTSHLGRPTEGEYNEEFSLLPVVNYLKDKLSNPVRLVKDYLDGVEVAAGELVVLENVRFNKGEKKDDEELSKKYAALCDVFVMDAFGTAHRAQASTHGIGKFADVACAGPLLAAELDALGKALKEPARPMVAIVGGSKVSTKLTVLDSLSKIADQLIVGGGIANTFVAAQGHNVGKSLYEADLVDEAKRLLGTCDIPVPTDVRVATEFSETATATLKSVNDIKDDEQILDLGDVSAQKLAEILKNAKTILWNGPVGVFEFPNFRKGTEIVANAIADSEGFSIAGGGDTLAAIDLFGIADKISYISTGGGAFLEFVEGKVLPAVAMLEERAKQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

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

Domain and signature matches imported from InterPro and related databases.

36 records
Show feature table
Start End DB Term Name
31 53 PRINTS PR00477 Phosphoglycerate kinase family signature
31 53 InterPro IPR001576 Phosphoglycerate kinase
336 347 PRINTS PR00477 Phosphoglycerate kinase family signature
336 347 InterPro IPR001576 Phosphoglycerate kinase
132 154 PRINTS PR00477 Phosphoglycerate kinase family signature
132 154 InterPro IPR001576 Phosphoglycerate kinase
359 376 PRINTS PR00477 Phosphoglycerate kinase family signature
359 376 InterPro IPR001576 Phosphoglycerate kinase
10 26 PRINTS PR00477 Phosphoglycerate kinase family signature
10 26 InterPro IPR001576 Phosphoglycerate kinase
163 185 PRINTS PR00477 Phosphoglycerate kinase family signature
163 185 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
303 328 PRINTS PR00477 Phosphoglycerate kinase family signature
303 328 InterPro IPR001576 Phosphoglycerate kinase
169 373 FunFam G3DSA:3.40.50.1260:FF:000001 Phosphoglycerate kinase
5 384 PANTHER PTHR11406 PHOSPHOGLYCERATE KINASE
5 384 InterPro IPR001576 Phosphoglycerate kinase
3 383 SUPERFAMILY SSF53748 Phosphoglycerate kinase
3 383 InterPro IPR036043 Phosphoglycerate kinase superfamily
165 373 Gene3D G3DSA:3.40.50.1260 -
165 373 InterPro IPR015824 Phosphoglycerate kinase, N-terminal
8 383 Hamap MF_00145 Phosphoglycerate kinase [pgk].
8 383 InterPro IPR001576 Phosphoglycerate kinase
8 381 Gene3D G3DSA:3.40.50.1260 -
8 381 InterPro IPR015824 Phosphoglycerate kinase, N-terminal
7 168 FunFam G3DSA:3.40.50.1260:FF:000002 Phosphoglycerate kinase
15 25 ProSitePatterns PS00111 Phosphoglycerate kinase signature.
15 25 InterPro IPR015911 Phosphoglycerate kinase, conserved site
1 387 PIRSF PIRSF000724 Pgk
1 387 InterPro IPR001576 Phosphoglycerate kinase
6 373 Pfam PF00162 Phosphoglycerate kinase
6 373 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 · FPocket

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

Site 1 FPocket #2
0.876
Likely same site as P2Rank 1 2.1 Å 15 shared residues 88% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.613
Likely same site as FPocket 2 2.1 Å 15 shared residues 88% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.12
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.119
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.069
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.044
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 KP13_02160
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.

153 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 103 records from similar proteins
Structural ligands 3 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
BTB PDB via homolog Detail RCSB PDB
C04 ChEMBL via homolog Detail ChEMBL
CHEMBL119171 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 P36204 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 Q04LZ5 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)…
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.