Protein profile

PA3896

2-hydroxyacid dehydrogenase

Genome: NC_002516.2

Gene: PA3896 Structure source: AlphaFold UniProt Q9HXB7
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Amino acids 325
Annotations 5
Features 14
PDB binders 8
Druggability 0.422

Overview

Basic information about this protein and its source genome.

Accession
PA3896
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA3896
Status
annotated
Amino acids
325
Structure source
AlphaFold
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:0030267 Catalysis of the reaction: glycolate + NADP+ = glyoxylate + NADPH + H+. GO:0016618 Catalysis of the reaction: (R)-glycerate + NAD(P)+ = 3-hydroxypyruvate + NAD(P)H + 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:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
43.952
Human E-value
7.61e-55
Gut microbiome off-target
hit
Essential (DEG)
Y
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 0.422
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0030267 Catalysis of the reaction: glycolate + NADP+ = glyoxylate + NADPH + H+.
  • GO:0016618 Catalysis of the reaction: (R)-glycerate + NAD(P)+ = 3-hydroxypyruvate + NAD(P)H + 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:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
226 242 ProSitePatterns PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
226 242 InterPro IPR029753 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
108 286 Pfam PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
108 286 InterPro IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
97 288 Gene3D G3DSA:3.40.50.720 -
5 313 Gene3D G3DSA:3.40.50.720 -
98 286 FunFam G3DSA:3.40.50.720:FF:000462 Glyoxylate reductase (NADP+)
4 314 PANTHER PTHR10996 2-HYDROXYACID DEHYDROGENASE-RELATED
3 310 CDD cd05301 GDH
100 287 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
100 287 InterPro IPR036291 NAD(P)-binding domain superfamily
1 133 SUPERFAMILY SSF52283 Formate/glycerate dehydrogenase catalytic domain-like
5 318 Pfam PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
5 318 InterPro IPR006139 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain

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 + 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 PA3896
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 0.422
2 0.207

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

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
8YV
5V7N
Q92LZ4 194.1 Da LogP -3.28 TPSA 135.3 ✓ Ro5 ✓ Clean C([C@H]([C@H]([C@@H](C(=O)C(=O)O)O)O)O)O
A2R
5J23
Q92LZ4 639.3 Da LogP -3.17 TPSA 338.0 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DGY
2GCG
Q9UBQ7 106.1 Da LogP -1.58 TPSA 77.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)O
GLV
5AOV
Q8U3Y2 74.0 Da LogP -0.73 TPSA 54.4 ✓ Ro5 ✓ Clean C(=O)C(=O)O
MLA
5V6Q
Q92LZ4 104.1 Da LogP -0.45 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)O)C(=O)O
MLI
6BII
F8AEA4 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
NHE
2CUK
Q5SMG6 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O
OXL
5V7G
Q92LZ4 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=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.