Protein target profile

PA1500

2-hydroxy-3-oxopropionate reductase

Genome: NC_002516.2

Gene: PA1500 3D evidence: AlphaFold DB model UniProt Q9I3L2
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Length 296
Pocket druggability 0.71
Ligand records 58
EC / GO 0 / 5
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

4 signals

Strengths

Strong predicted binding pocket FPocket selected-pocket score 0.71. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model Ligand evidence via structure/bioactivity 8 structural and 0 bioactivity records.

Risks / watch

Human similarity Top human hit identity: 35.57%.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
How to read 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 TPW 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.

Overview

Basic information about this protein and its source genome.

Accession
PA1500
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA1500
Status
annotated
Amino acids
296
3D evidence
AlphaFold DB model
GO
GO:0008679 Catalysis of the reaction: (R)-glycerate + NADP+ = 2-hydroxy-3-oxopropanoate + NADPH + H+. GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH. GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH. GO:0046487 The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Target profile

Computed evidence for target prioritization.

Human off-target
Hit
Human identity (%)
35.57
Human E-value
1.05e-24
Gut microbiome off-target
Hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected pocket evidence

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 0.71
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MAKIGFIGTGIMGKPMAQNLQKAGHSLFLSTHHDAAPADLLEAGAIALANPKEVAQEAEFIIVMVPDTPQVEDVLFRKDGIAEGAGPNKVVIDMSSISPTATKGFAEKIKATGAQYLDAPVSGGEVGAKAATLSIMVGGCPNTFERALPLFQAMGKNITRVGGNGDGQTAKVANQIIVALNIQAVAEALLFAARNGADPAKVREALMGGFASSRILEVHGERMVKGTFDPGFRISLHQKDLNLALAGARELNLNLPNTANAQQVFSTCAAIGGSNWDHSALIKGLEHMANFSIRDE

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0008679 Catalysis of the reaction: (R)-glycerate + NADP+ = 2-hydroxy-3-oxopropanoate + NADPH + H+.
  • GO:0051287 Binding to nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
  • GO:0050661 Binding to nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
  • GO:0046487 The chemical reactions and pathways involving glyoxylate, the anion of glyoxylic acid, HOC-COOH.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
2 162 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
2 162 InterPro IPR036291 NAD(P)-binding domain superfamily
163 291 Gene3D G3DSA:1.10.1040.10 -
163 291 InterPro IPR013328 6-phosphogluconate dehydrogenase, domain 2
165 283 Pfam PF14833 NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
165 283 InterPro IPR029154 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain
1 291 PIRSF PIRSF000103 HIBADH
1 291 InterPro IPR015815 3-hydroxyisobutyrate dehydrogenase-related
2 293 PANTHER PTHR43060 3-HYDROXYISOBUTYRATE DEHYDROGENASE-LIKE 1, MITOCHONDRIAL-RELATED
3 291 NCBIfam TIGR01505 2-hydroxy-3-oxopropionate reductase
3 291 InterPro IPR006398 2-hydroxy-3-oxopropionate reductase
164 291 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
164 291 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
3 162 Pfam PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase
3 162 InterPro IPR006115 6-phosphogluconate dehydrogenase, NADP-binding
1 162 Gene3D G3DSA:3.40.50.720 -

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.

3D visualization script Full viewer

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Structural evidence

0 + 1

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 PA1500
AlphaFold DB — — full sequence — Viewing
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 #4
0.71
Show in viewer
Site 2 FPocket #1
0.703
Show in viewer

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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 58 via homologs
Structural ligands 8 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 40 0 PAINS alerts
Best available ligand signal
3OH PDB via homolog 90.1 Da · LogP -0.55 · TPSA 57.5 Open detail RCSB PDB
Detail RCSB PDB 3OH PDB via homolog
Detail RCSB PDB 9ON PDB via homolog
Detail RCSB PDB AKR PDB via homolog
Detail RCSB PDB BO3 PDB via homolog

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
3OH RCSB PDB
5Y8O
P9WNY5 90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C(CO)C(=O)O
9ON RCSB PDB
5Y8L
P9WNY5 146.1 Da LogP 0.57 TPSA 74.6 ✓ Ro5 ✓ Clean C[C@@H](CCC(=O)O)C(=O)O
AKR RCSB PDB
5Y8M
P9WNY5 72.1 Da LogP 0.26 TPSA 37.3 ✓ Ro5 ✓ Clean C=CC(=O)O
BO3 RCSB PDB
6SM7
P0A9V8 61.8 Da LogP -2.05 TPSA 60.7 ✓ Ro5 ✓ Clean B(O)(O)O
HIU RCSB PDB
5Y8M
P9WNY5 104.1 Da LogP -0.30 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@H](CO)C(=O)O
HUI RCSB PDB
5Y8L
P9WNY5 104.1 Da LogP -0.30 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@@H](CO)C(=O)O
LLQ RCSB PDB
6SMY
P0A9V8 156.2 Da LogP -1.77 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](CS(=O)(=O)O)O)O
TLA RCSB PDB
5XVH
A3MU08 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=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.