Protein profile

KP13_02991

2,3-bisphosphoglycerate-dependent phosphoglycerate mutase

Genome: KpKP13

Gene: gpmA AHE45626.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU79
Export view
Amino acids 250
Annotations 6
Features 21
PDB binders 9
Druggability 0.181

Overview

Basic information about this protein and its source genome.

Accession
KP13_02991
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
gpmA AHE45626.1
Status
annotated
Amino acids
250
Structure source
AlphaFold + ColabFold
EC
5.4.2.11
GO
GO:0016868 Catalysis of the transfer of a phosphate group from one position to another within a single molecule. 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. 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:0004619 Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate. GO:0006094 The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
58.103
Human E-value
3.47e-101
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
59.677
DEG E-value
1.01e-111
Localization
Cytoplasmic
ColabFold pLDDT
96.01

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 0.181
Structure A0A0H3GU79
Pocket Pocket 4
P2Rank 0.808
Structure A0A0H3GU79
Pocket Pocket 1
ColabFold model
FPocket 0.274 · Pocket 5
P2Rank 0.786 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1226 / 4744 genomes with a hit
Normalized 0.258

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0016868 Catalysis of the transfer of a phosphate group from one position to another within a single molecule.
  • 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.
  • 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:0004619 Catalysis of the reaction: (2R)-2-phosphoglycerate = (2R)-3-phosphoglycerate.
  • GO:0006094 The formation of glucose from noncarbohydrate precursors, such as pyruvate, amino acids and glycerol.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
3 230 Hamap MF_01039 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase [gpmA].
3 230 InterPro IPR005952 Phosphoglycerate mutase 1
5 191 SMART SM00855 PGAM_5
5 191 InterPro IPR013078 Histidine phosphatase superfamily, clade-1
5 230 CDD cd07067 HP_PGM_like
5 230 InterPro IPR013078 Histidine phosphatase superfamily, clade-1
167 239 PIRSF PIRSF000709 6PFK_fruc_bisph_Ptase
3 116 PIRSF PIRSF000709 6PFK_fruc_bisph_Ptase
8 17 ProSitePatterns PS00175 Phosphoglycerate mutase family phosphohistidine signature.
8 17 InterPro IPR001345 Phosphoglycerate/bisphosphoglycerate mutase, active site
4 248 PANTHER PTHR11931 PHOSPHOGLYCERATE MUTASE
4 248 InterPro IPR005952 Phosphoglycerate mutase 1
4 247 SUPERFAMILY SSF53254 Phosphoglycerate mutase-like
4 247 InterPro IPR029033 Histidine phosphatase superfamily
2 250 FunFam G3DSA:3.40.50.1240:FF:000003 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
2 250 Gene3D G3DSA:3.40.50.1240 -
2 250 InterPro IPR029033 Histidine phosphatase superfamily
5 248 NCBIfam TIGR01258 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase
5 248 InterPro IPR005952 Phosphoglycerate mutase 1
6 221 Pfam PF00300 Histidine phosphatase superfamily (branch 1)
6 221 InterPro IPR013078 Histidine phosphatase superfamily, clade-1

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...

Legend High Medium Low

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_A0A0H3GU79
AlphaFold — — full sequence — Viewing
ColabFold KP13_02991
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 14.48 0.724
2 1.68 0.029

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.

86 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
3GP5
Q3JWH7 186.1 Da LogP -1.46 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)OP(=O)(O)O
9JF
5ZS8
P18669 411.4 Da LogP 2.38 TPSA 141.0 ✓ Ro5 Alert c1ccc2c(c1)C(=O)c3cc(c(c(c3C2=O)O)O)NS(=O)(=O)c…
AZN
5Y2U
P18669 320.3 Da LogP 1.12 TPSA 129.0 ✓ Ro5 Alert c1ccc2c(c1)C(=O)c3cc(c(c(c3C2=O)O)O)S(=O)(=O)O
MLI
3LNT
Q3JWH7 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
PG6
3GP5
Q3JWH7 266.3 Da LogP 0.35 TPSA 55.4 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOC
PO3
3GP3
Q3JWH7 79.0 Da LogP -1.64 TPSA 63.2 ✓ Ro5 ✓ Clean [O-][P-](=O)[O-]
SEP
3GP3
Q3JWH7 185.1 Da LogP -1.49 TPSA 130.1 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)OP(=O)(O)O
TLA
5UM0
B4RIY7 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
VO4
3GP5
Q3JWH7 114.9 Da LogP -3.69 TPSA 86.2 ✓ Ro5 ✓ Clean [O-][V](=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.