Protein profile

KP13_00708

Phosphoglycolate phosphatase

Genome: KpKP13

Gene: gph AHE42326.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GZE3
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Amino acids 253
Annotations 7
Features 30
PDB binders 6
Druggability 0.896

Overview

Basic information about this protein and its source genome.

Accession
KP13_00708
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
gph AHE42326.1
Status
annotated
Amino acids
253
Structure source
AlphaFold + ColabFold
EC
3.1.3.18
GO
GO:0008967 Catalysis of the reaction: 2-phosphoglycolate + H2O = glycolate + phosphate. GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0046872 Binding to a metal ion. GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway. GO:0046295 The chemical reactions and pathways resulting in the formation of glycolate, the anion of hydroxyethanoic acid (glycolic acid).

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.02

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 0.896
Structure A0A0H3GZE3
Pocket Pocket 1
P2Rank 0.341
Structure A0A0H3GZE3
Pocket Pocket 1
ColabFold model
FPocket 0.797 · Pocket 1
P2Rank 0.201 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 110 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

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:0008967 Catalysis of the reaction: 2-phosphoglycolate + H2O = glycolate + phosphate.
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0046872 Binding to a metal ion.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0046295 The chemical reactions and pathways resulting in the formation of glycolate, the anion of hydroxyethanoic acid (glycolic acid).

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
108 231 FunFam G3DSA:3.40.50.1000:FF:000022 Phosphoglycolate phosphatase
9 237 CDD cd16417 HAD_PGPase
7 241 Hamap MF_00495 Phosphoglycolate phosphatase [gph].
7 241 InterPro IPR037512 Phosphoglycolate phosphatase, prokaryotic
89 210 NCBIfam TIGR01509 HAD-IA family hydrolase
89 210 InterPro IPR006439 HAD hydrolase, subfamily IA
4 240 SUPERFAMILY SSF56784 HAD-like
4 240 InterPro IPR036412 HAD-like superfamily
10 240 NCBIfam TIGR01449 phosphoglycolate phosphatase
10 240 InterPro IPR037512 Phosphoglycolate phosphatase, prokaryotic
7 18 PRINTS PR00413 Haloacid dehalogenase/epoxide hydrolase family signature
7 18 InterPro IPR006439 HAD hydrolase, subfamily IA
173 193 PRINTS PR00413 Haloacid dehalogenase/epoxide hydrolase family signature
173 193 InterPro IPR006439 HAD hydrolase, subfamily IA
124 137 PRINTS PR00413 Haloacid dehalogenase/epoxide hydrolase family signature
124 137 InterPro IPR006439 HAD hydrolase, subfamily IA
155 171 PRINTS PR00413 Haloacid dehalogenase/epoxide hydrolase family signature
155 171 InterPro IPR006439 HAD hydrolase, subfamily IA
7 240 SFLD SFLDG01135 C1.5.6: HAD, Beta-PGM, Phosphatase Like
10 209 Pfam PF13419 Haloacid dehalogenase-like hydrolase
10 209 InterPro IPR041492 Haloacid dehalogenase-like hydrolase
125 205 NCBIfam TIGR01549 HAD-IA family hydrolase
125 205 InterPro IPR006439 HAD hydrolase, subfamily IA
8 238 PANTHER PTHR43434 PHOSPHOGLYCOLATE PHOSPHATASE
22 110 Gene3D G3DSA:1.10.150.240 Putative phosphatase; domain 2
22 110 InterPro IPR023198 Phosphoglycolate phosphatase-like, domain 2
10 231 Gene3D G3DSA:3.40.50.1000 -
10 231 InterPro IPR023214 HAD superfamily
7 240 SFLD SFLDS00003 Haloacid Dehalogenase
22 110 FunFam G3DSA:1.10.150.240:FF:000003 Phosphoglycolate phosphatase

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

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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_A0A0H3GZE3
AlphaFold — — full sequence — Viewing
ColabFold KP13_00708
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
1 0.896

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 3.04 0.1
2 1.67 0.028

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.

56 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
AC0
6Q7N
O58216 120.2 Da LogP 1.89 TPSA 17.1 ✓ Ro5 ✓ Clean CC(=O)c1ccccc1
BO3
4EX7
B6SEG4 61.8 Da LogP -2.05 TPSA 60.7 ✓ Ro5 ✓ Clean B(O)(O)O
NHE
4YGR
B6YTD6 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
PGA
1TE2
P77247 156.0 Da LogP -0.82 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)O)OP(=O)(O)O
TBU
4YGQ
B6YTD6 74.1 Da LogP 0.78 TPSA 20.2 ✓ Ro5 ✓ Clean CC(C)(C)O
XBP
4UAT
P95649 310.1 Da LogP -2.50 TPSA 191.0 1 viol. ✓ Clean C([C@H]([C@@H](C(=O)COP(=O)(O)O)O)O)OP(=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.