KpKP13 Protein target profile

2-hydroxy-3-oxopropionate reductase

Accession: KP13_01072

Gene: AHE42535.1 garR 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GTL6
Length 302
Pocket druggability (P2Rank · AlphaFold DB model) 0.907
Direct ligand evidence 0 59 total records
Functional annotation 1 EC 6 GO
Target summary

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

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on 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 Target 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.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
36.842 Lower values reduce human off-target concern.
Human E-value
1.11e-26
Gut microbiome similarity
6.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
96.56 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.907
Structure A0A0H3GTL6
Pocket Pocket 1
Druggability (FPocket) 0.239
Structure A0A0H3GTL6
Pocket Pocket 9
ColabFold model
P2Rank 0.927 · Pocket 1
FPocket 0.789 · Pocket 13
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 283 / 4744 genomes with a hit
Prevalence 6.0%

Sequence

Primary amino-acid sequence viewer.

MKRENIMTIKVGFIGLGIMGKPMSKNLLKAGYSLVVSDRNPEAIADVIAAGAETATTPKAIAEQCEVIITMLPNSPHVKEVALGENGIIEGAKPGTVVIDMSSIAPLASREISEALKAKGIDMLDAPVSGGEPKAIDGTLSVMVGGDKAIFDKYYDLMKAMAGSVVHTGDIGAGNVTKLANQVIVALNIAAMSEALTLATKAGVNPDLVYQAIRGGLAGSTVLDAKAPMVMDRNFKPGFRIDLHIKDLANALDTSHGVGAQLPLTAAVMEMMQALRADGLGTADHSALACYYEKLAKVEVTR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • 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: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.
  • 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:0046392 The chemical reactions and pathways resulting in the breakdown of D-galactarate, the anion of galactaric acid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
9 170 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
9 170 InterPro IPR036291 NAD(P)-binding domain superfamily
13 26 ProSitePatterns PS00895 3-hydroxyisobutyrate dehydrogenase signature.
13 26 InterPro IPR002204 3-hydroxyisobutyrate dehydrogenase-related, conserved site
172 302 FunFam G3DSA:1.10.1040.10:FF:000008 2-hydroxy-3-oxopropionate reductase
5 171 Gene3D G3DSA:3.40.50.720 -
10 300 NCBIfam TIGR01505 2-hydroxy-3-oxopropionate reductase
10 300 InterPro IPR006398 2-hydroxy-3-oxopropionate reductase
172 289 Pfam PF14833 NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase
172 289 InterPro IPR029154 3-hydroxyisobutyrate dehydrogenase-like, NAD-binding domain
7 300 PANTHER PTHR43060 3-HYDROXYISOBUTYRATE DEHYDROGENASE-LIKE 1, MITOCHONDRIAL-RELATED
7 171 FunFam G3DSA:3.40.50.720:FF:000071 2-hydroxy-3-oxopropionate reductase
10 169 Pfam PF03446 NAD binding domain of 6-phosphogluconate dehydrogenase
10 169 InterPro IPR006115 6-phosphogluconate dehydrogenase, NADP-binding
9 302 Hamap MF_02032 2-hydroxy-3-oxopropionate reductase [garR].
9 302 InterPro IPR006398 2-hydroxy-3-oxopropionate reductase
3 301 PIRSF PIRSF000103 HIBADH
3 301 InterPro IPR015815 3-hydroxyisobutyrate dehydrogenase-related
170 299 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
170 299 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
172 302 Gene3D G3DSA:1.10.1040.10 -
172 302 InterPro IPR013328 6-phosphogluconate dehydrogenase, domain 2

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.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.907
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.196
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.017
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #9
0.239
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:152-152
UniProt: Binding site:220-220
UniProt: Binding site:77-77
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

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 AF_A0A0H3GTL6
AlphaFold DB full sequence Viewing
ColabFold KP13_01072
ColabFold full sequence Loaded

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.

59 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 9 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3OH PDB via homolog 90.1 Da · LogP -0.55 · TPSA 57.5 Open detail RCSB PDB
7VD PDB via homolog Detail RCSB PDB
9ON PDB via homolog Detail RCSB PDB
AKR PDB via homolog Detail RCSB PDB
BO3 PDB via homolog Detail RCSB PDB

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 P9WNY5 90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C(CO)C(=O)O
7VD RCSB PDB I6R485 138.1 Da LogP -0.25 TPSA 74.6 ✓ Ro5 ✓ Clean CC(=O)CP(=O)(O)O
9ON RCSB PDB P9WNY5 146.1 Da LogP 0.57 TPSA 74.6 ✓ Ro5 ✓ Clean C[C@@H](CCC(=O)O)C(=O)O
AKR RCSB PDB P9WNY5 72.1 Da LogP 0.26 TPSA 37.3 ✓ Ro5 ✓ Clean C=CC(=O)O
BO3 RCSB PDB P0A9V8 61.8 Da LogP -2.05 TPSA 60.7 ✓ Ro5 ✓ Clean B(O)(O)O
HIU RCSB PDB P9WNY5 104.1 Da LogP -0.30 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@H](CO)C(=O)O
HUI RCSB PDB P9WNY5 104.1 Da LogP -0.30 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@@H](CO)C(=O)O
LLQ RCSB PDB P0A9V8 156.2 Da LogP -1.77 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@@H](CS(=O)(=O)O)O)O
TLA RCSB PDB Q8ZLV8 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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.