Protein profile

KP13_03372

putative 2-hydroxyacid dehydrogenase

Genome: KpKP13

Gene: AHE45751.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GPT4
Amino acids 342
Annotations 5
Features 12
PDB binders 19
Druggability 0.548

Overview

Basic information about this protein and its source genome.

Accession
KP13_03372
Gene
AHE45751.1
Status
annotated
Amino acids
342
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
41.732
Human E-value
2.65e-24
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.25

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 0.548
Structure A0A0H3GPT4
Pocket Pocket 8
P2Rank 0.872
Structure A0A0H3GPT4
Pocket Pocket 1
ColabFold model
FPocket 0.698 · Pocket 6
P2Rank 0.868 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 15 / 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.

5 GO

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:0047545 Catalysis of the reaction: (S)-2-hydroxyglutarate + acceptor = 2-oxoglutarate + reduced acceptor.
  • GO:0004617 Catalysis of the reaction: 3-phosphoglycerate + NAD+ = 3-phosphohydroxypyruvate + NADH + H+.
  • GO:0006564 The chemical reactions and pathways resulting in the formation of L-serine.

Sequence Features

Domain/signature hits from InterPro and related databases.

12 records
Show feature table
Start End DB Term Name
1 332 CDD cd12171 2-Hacid_dh_10
31 335 Gene3D G3DSA:3.40.50.720 -
34 337 PANTHER PTHR42789 D-ISOMER SPECIFIC 2-HYDROXYACID DEHYDROGENASE FAMILY PROTEIN (AFU_ORTHOLOGUE AFUA_6G10090)
108 310 Pfam PF02826 D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain
108 310 InterPro IPR006140 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding domain
29 132 SUPERFAMILY SSF52283 Formate/glycerate dehydrogenase catalytic domain-like
33 337 Pfam PF00389 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
33 337 InterPro IPR006139 D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain
99 311 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
99 311 InterPro IPR036291 NAD(P)-binding domain superfamily
100 313 FunFam G3DSA:3.40.50.720:FF:000041 D-3-phosphoglycerate dehydrogenase
97 312 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

Loading 3D structure...

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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_A0A0H3GPT4
AlphaFold full sequence Viewing
ColabFold KP13_03372
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
2 0.043
11 0.02
12 0.001
18 0.001

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 26.24 0.872
2 2.05 0.038
3 1.47 0.017

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…
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.