Protein profile

PA4626

glycerate dehydrogenase

Genome: NC_002516.2

Gene: PA4626 hprA Structure source: AlphaFold UniProt Q9HVG5
Amino acids 323
Annotations 2
Features 13
PDB binders 19
Druggability 0.767

Overview

Basic information about this protein and its source genome.

Accession
PA4626
Gene
PA4626 hprA
Status
annotated
Amino acids
323
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
46.853
Human E-value
1.64e-22
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 0.767
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • 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.

13 records
Show feature table
Start End DB Term Name
1 321 PANTHER PTHR43761 D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE FAMILY PROTEIN (AFU_ORTHOLOGUE AFUA_1G13630)
112 290 Pfam PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
112 290 InterPro IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
106 291 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
106 291 InterPro IPR036291 NAD(P)-binding domain superfamily
5 311 CDD cd12162 2-Hacid_dh_4
19 320 Pfam PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
19 320 InterPro IPR006139 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
227 243 ProSitePatterns PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
227 243 InterPro IPR029753 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
20 317 Gene3D G3DSA:3.40.50.720 -
17 141 SUPERFAMILY SSF52283 Formate/glycerate dehydrogenase catalytic domain-like
102 289 Gene3D G3DSA:3.40.50.720 -

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 PA4626
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
1 0.767

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.

169 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
3PG O43175 186.1 Da LogP -1.46 TPSA 124.3 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)OP(=O)(O)O
5AO O43175 160.2 Da LogP 1.92 TPSA 52.0 ✓ Ro5 ✓ Clean c1cc(cc(c1)N)c2cnco2
8NB O43175 199.6 Da LogP 2.31 TPSA 38.3 ✓ Ro5 ✓ Clean CC(=O)Nc1ccc(c(c1)Cl)OC
9EW O43175 135.1 Da LogP 1.53 TPSA 46.3 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(no2)O
9EZ O43175 173.2 Da LogP 1.67 TPSA 43.8 ✓ Ro5 ✓ Clean Cn1c(cc(n1)c2ccccc2)N
9TT O43175 146.2 Da LogP 1.76 TPSA 30.9 ✓ Ro5 Alert Cn1ccc2c1ccc(c2)N
9TW O43175 173.6 Da LogP 1.58 TPSA 43.1 ✓ Ro5 ✓ Clean c1cc(c(cc1C(=O)N)Cl)F
9TZ O43175 154.1 Da LogP 1.83 TPSA 37.3 ✓ Ro5 ✓ Clean Cc1ccc(cc1C(=O)O)F
AKG P0A9T0 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
GLV Q8U3Y2 74.0 Da LogP -0.73 TPSA 54.4 ✓ Ro5 ✓ Clean C(=O)C(=O)O
HMT O43175 545.6 Da LogP 2.58 TPSA 124.0 1 viol. ✓ Clean CC(C)(CCC[C@@](CC(=O)OC)(C(=O)O[C@H]1[C@H]2c3cc…
HPV P9WNX3 184.0 Da LogP -1.25 TPSA 121.1 ✓ Ro5 ✓ Clean C(C(=O)C(=O)O)OP(=O)(O)O
K4T O43175 241.3 Da LogP 1.98 TPSA 46.9 ✓ Ro5 ✓ Clean Cn1c(cc(n1)c2ccccc2)C(=O)NC3CC3
K5N O43175 426.5 Da LogP 2.27 TPSA 110.2 ✓ Ro5 ✓ Clean C[C@H](c1ccc(cc1)C(=O)NS(=O)(=O)C)NC(=O)c2cc(nn…
LAC O66939 90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@H](C(=O)O)O
MLT O43175 134.1 Da LogP -1.09 TPSA 94.8 ✓ Ro5 ✓ Clean C([C@H](C(=O)O)O)C(=O)O
ONS O43175 510.4 Da LogP 4.75 TPSA 93.5 1 viol. ✓ Clean Cn1c2ccc(c(c2cc1C(=O)NC3(COC3)c4ccc(cc4)[C@@H](…
PPI O66939 74.1 Da LogP 0.48 TPSA 37.3 ✓ Ro5 ✓ Clean CCC(=O)O
TLA O43175 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.