Protein profile

VK055_0864

glyoxylate reductase

Genome: KpATCC43816

Gene: gyaR AIK79487.1 Structure source: AlphaFold + ColabFold UniProt A0A0C7KEI7
Amino acids 316
Annotations 6
Features 16
PDB binders 19
Druggability 0.82

Overview

Basic information about this protein and its source genome.

Accession
VK055_0864
Gene
gyaR AIK79487.1
Status
annotated
Amino acids
316
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
44.304
Human E-value
9.47e-16
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
41.6
DEG E-value
3.0000000000000003e-56
Localization
Cytoplasmic
ColabFold pLDDT
96.65

Selected Druggability evidence

AlphaFold / UniProt model

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 0.82
Structure A0A0C7KEI7
Pocket Pocket 15
P2Rank 0.962
Structure A0A0C7KEI7
Pocket Pocket 1
ColabFold model
FPocket 0.296 · Pocket 19
P2Rank 0.915 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 9 / 4744 genomes with a hit
Normalized 0.002

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • 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.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004617 Catalysis of the reaction: 3-phosphoglycerate + NAD+ = 3-phosphohydroxypyruvate + NADH + H+.
  • GO:0008652 The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
109 281 Pfam PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
109 281 InterPro IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
221 237 ProSitePatterns PS00671 D-isomer specific 2-hydroxyacid dehydrogenases signature 3.
221 237 InterPro IPR029753 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site
16 314 Pfam PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
16 314 InterPro IPR006139 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
35 305 PANTHER PTHR10996 2-HYDROXYACID DEHYDROGENASE-RELATED
2 301 CDD cd12172 PGDH_like_2
23 314 Gene3D G3DSA:3.40.50.720 -
98 281 Gene3D G3DSA:3.40.50.720 -
99 282 FunFam G3DSA:3.40.50.720:FF:000203 D-3-phosphoglycerate dehydrogenase (SerA)
144 171 ProSitePatterns PS00065 D-isomer specific 2-hydroxyacid dehydrogenases NAD-binding signature.
144 171 InterPro IPR029752 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain conserved site 1
100 282 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
100 282 InterPro IPR036291 NAD(P)-binding domain superfamily
2 133 SUPERFAMILY SSF52283 Formate/glycerate dehydrogenase catalytic domain-like

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 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0C7KEI7
AlphaFold full sequence Viewing
ColabFold VK055_0864
ColabFold full sequence Loaded
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
15 0.82
2 0.303
14 0.296

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 27.29 0.92
2 1.03 0.006

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
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
K5K O43175 499.4 Da LogP 3.12 TPSA 125.7 ✓ Ro5 ✓ Clean Cc1cc2c(cc(n2C)C(=O)N[C@H](CO)c3ccc(cc3)S(=O)(=…
LAC O66939 90.1 Da LogP -0.55 TPSA 57.5 ✓ Ro5 ✓ Clean C[C@H](C(=O)O)O
MLI F8AEA4 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=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.