Protein profile

PA0608

phosphoglycolate phosphatase

Genome: NC_002516.2

Gene: gph1 PA0608 Structure source: AlphaFold UniProt Q9S586
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Amino acids 272
Annotations 7
Features 29
PDB binders 5
Druggability 0.686

Overview

Basic information about this protein and its source genome.

Accession
PA0608
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
gph1 PA0608
Status
annotated
Amino acids
272
Structure source
AlphaFold
EC
3.1.3.18
GO
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: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: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
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected Druggability evidence

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 0.686
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MSAAEPFFATRLPRLVMFDLDGTLVDSVPDLTAAVDSMLASFGRPPAGIEKVRQWIGNGARVLVRRALAGSIEHDGIGEEETEAALALFMEAYADSHALTEVYPGVVDTLKWLKRNGVEMALITNKPERFVAPLLDEMKLGRYFRWIIGGDTLPQQKPDPAALLFVMKMAGIEPEDALFVGDSRNDVLAAKAAGVRCAALTYGYNHGRPIAEEAPTLVIDNLRDLLPCADQAAEIVLPDDSLSPSDQRDQAVAVSKLWMKVIKALARWRWRA

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: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: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: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.

29 records
Show feature table
Start End DB Term Name
14 227 SFLD SFLDG01135 C1.5.6: HAD, Beta-PGM, Phosphatase Like
13 230 Hamap MF_00495 Phosphoglycolate phosphatase [gph].
13 230 InterPro IPR037512 Phosphoglycolate phosphatase, prokaryotic
94 220 FunFam G3DSA:3.40.50.1000:FF:000022 Phosphoglycolate phosphatase
13 226 SUPERFAMILY SSF56784 HAD-like
13 226 InterPro IPR036412 HAD-like superfamily
16 220 Gene3D G3DSA:3.40.50.1000 -
16 220 InterPro IPR023214 HAD superfamily
114 194 NCBIfam TIGR01549 HAD-IA family hydrolase
114 194 InterPro IPR006439 HAD hydrolase, subfamily IA
113 126 PRINTS PR00413 Haloacid dehalogenase/epoxide hydrolase family signature
113 126 InterPro IPR006439 HAD hydrolase, subfamily IA
13 24 PRINTS PR00413 Haloacid dehalogenase/epoxide hydrolase family signature
13 24 InterPro IPR006439 HAD hydrolase, subfamily IA
144 160 PRINTS PR00413 Haloacid dehalogenase/epoxide hydrolase family signature
144 160 InterPro IPR006439 HAD hydrolase, subfamily IA
162 182 PRINTS PR00413 Haloacid dehalogenase/epoxide hydrolase family signature
162 182 InterPro IPR006439 HAD hydrolase, subfamily IA
16 227 NCBIfam TIGR01449 phosphoglycolate phosphatase
16 227 InterPro IPR037512 Phosphoglycolate phosphatase, prokaryotic
15 226 CDD cd16417 HAD_PGPase
28 99 Gene3D G3DSA:1.10.150.240 Putative phosphatase; domain 2
28 99 InterPro IPR023198 Phosphoglycolate phosphatase-like, domain 2
14 227 SFLD SFLDS00003 Haloacid Dehalogenase
92 197 NCBIfam TIGR01509 HAD-IA family hydrolase
92 197 InterPro IPR006439 HAD hydrolase, subfamily IA
16 199 Pfam PF13419 Haloacid dehalogenase-like hydrolase
16 199 InterPro IPR041492 Haloacid dehalogenase-like hydrolase
3 227 PANTHER PTHR43434 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.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA0608
AlphaFold — — full sequence — Viewing
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
3 0.686
2 0.378

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.

44 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
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.