Protein profile

VK055_2302

D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain protein

Genome: KpATCC43816

Gene: AIK80906.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GNS1
Amino acids 331
Annotations 2
Features 12
PDB binders 17
Druggability 0.372

Overview

Basic information about this protein and its source genome.

Accession
VK055_2302
Gene
AIK80906.1
Status
annotated
Amino acids
331
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
41.975
Human E-value
7.22e-09
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
39.608
Localization
Cytoplasmic
ColabFold pLDDT
96.28

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 0.372
Structure A0A0H3GNS1
Pocket Pocket 13
P2Rank 0.872
Structure A0A0H3GNS1
Pocket Pocket 1
ColabFold model
FPocket 0.232 · Pocket 18
P2Rank 0.869 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 14 / 4744 genomes with a hit
Normalized 0.003

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.

12 records
Show feature table
Start End DB Term Name
28 330 CDD cd12171 2-Hacid_dh_10
123 309 FunFam G3DSA:3.40.50.720:FF:000203 D-3-phosphoglycerate dehydrogenase (SerA)
133 308 Pfam PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
133 308 InterPro IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
41 132 Pfam PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
41 132 InterPro IPR006139 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
59 318 PANTHER PTHR43761 D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE FAMILY PROTEIN (AFU_ORTHOLOGUE AFUA_1G13630)
39 317 Gene3D G3DSA:3.40.50.720 -
120 310 Gene3D G3DSA:3.40.50.720 -
127 309 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
127 309 InterPro IPR036291 NAD(P)-binding domain superfamily
55 160 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_A0A0H3GNS1
AlphaFold full sequence Viewing
ColabFold VK055_2302
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
13 0.372
2 0.175
1 0.0
12 0.0

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 26.3 0.872
2 0.84 0.003

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.

167 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
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
NHE Q5SMG6 207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=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](…
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.