Protein profile

VK055_4127

phosphoglycerate kinase family protein

Genome: KpATCC43816

Gene: AIK82673.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H2Q3
Amino acids 382
Annotations 2
Features 36
PDB binders 4
Druggability 0.876

Overview

Basic information about this protein and its source genome.

Accession
VK055_4127
Gene
AIK82673.1
Status
annotated
Amino acids
382
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
38.424
Human E-value
9.58e-76
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
96.335
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.54

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 0.876
Structure A0A0H3H2Q3
Pocket Pocket 2
P2Rank 0.613
Structure A0A0H3H2Q3
Pocket Pocket 1
ColabFold model
FPocket 0.374 · Pocket 2
P2Rank 0.545 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 304 / 4744 genomes with a hit
Normalized 0.064

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

3D visualization script Full viewer

Loading 3D structure...

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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_A0A0H3H2Q3
AlphaFold full sequence Viewing
ColabFold VK055_4127
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
2 0.876

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 9.99 0.537
2 2.11 0.048
3 1.91 0.039

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

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 P07378 186.1 Da LogP -1.46 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)OP(=O)(O)O
ANP 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 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 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.