Protein profile

VK055_3235

glycerol dehydrogenase

Genome: KpATCC43816

Gene: AIK81796.1 dhaD2 Structure source: Experimental + ColabFold UniProt A6TGD6
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Amino acids 367
Annotations 3
Features 16
PDB binders 4
Druggability 0.857

Overview

Basic information about this protein and its source genome.

Accession
VK055_3235
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK81796.1 dhaD2
Status
annotated
Amino acids
367
Structure source
Experimental + ColabFold
GO
GO:0016614 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor. GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced. GO:0046872 Binding to a metal ion.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.28

Selected Druggability evidence

PDB experimental structure

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 0.857
Structure 8K1H
Pocket Pocket 1
P2Rank 0.965
Structure 8K1H
Pocket Pocket 1
ColabFold model
FPocket 0.379 · Pocket 18
P2Rank 0.952 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 740 / 4744 genomes with a hit
Normalized 0.156

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0016614 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0046872 Binding to a metal ion.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
2 361 PANTHER PTHR43616 GLYCEROL DEHYDROGENASE
2 361 InterPro IPR016205 Glycerol dehydrogenase
160 367 FunFam G3DSA:1.20.1090.10:FF:000004 Glycerol dehydrogenase
3 355 SUPERFAMILY SSF56796 Dehydroquinate synthase-like
241 261 ProSitePatterns PS00060 Iron-containing alcohol dehydrogenases signature 2.
241 261 InterPro IPR018211 Alcohol dehydrogenase, iron-type, conserved site
8 347 Pfam PF00465 Iron-containing alcohol dehydrogenase
8 347 InterPro IPR001670 Alcohol dehydrogenase, iron-type/glycerol dehydrogenase GldA
1 360 PIRSF PIRSF000112 Glycerol_dh
1 360 InterPro IPR016205 Glycerol dehydrogenase
1 159 Gene3D G3DSA:3.40.50.1970 -
8 358 CDD cd08170 GlyDH
150 178 ProSitePatterns PS00913 Iron-containing alcohol dehydrogenases signature 1.
150 178 InterPro IPR018211 Alcohol dehydrogenase, iron-type, conserved site
1 159 FunFam G3DSA:3.40.50.1970:FF:000005 Glycerol dehydrogenase
160 367 Gene3D G3DSA:1.20.1090.10 -

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

1 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 8K1H
X-ray 20.00 Å - —
PDBe RCSB PDBj File
Viewing
ColabFold VK055_3235
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
1 0.857
2 0.492

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 40.88 0.965

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.

54 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
13P
4RGQ
Q58122 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)COP(=O)(O)O)O
1GP
4RGQ
Q58122 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@@H](COP(=O)(O)O)O)O
APR
1RRM
P0A9S1 559.3 Da LogP -3.28 TPSA 291.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
PPV
5FB3
A3MTM6 178.0 Da LogP -0.81 TPSA 124.3 ✓ Ro5 ✓ Clean OP(=O)(O)OP(=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.