KpKP13 Protein target profile

Glycerol dehydrogenase

Accession: KP13_00562

Gene: gldA AHE47037.1 3D evidence: Experimental + ColabFold model UniProt A6TGD6
Length 367
Pocket druggability (P2Rank · Experimental) 0.965
Direct ligand evidence 0 54 total records
Functional annotation 0 EC 3 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
15.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
97.23 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.965
Structure 8K1H
Pocket Pocket 1
Druggability (FPocket) 0.857
Structure 8K1H
Pocket Pocket 1
ColabFold model
P2Rank 0.952 · Pocket 1
FPocket 0.314 · Pocket 18
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 741 / 4744 genomes with a hit
Prevalence 15.6%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

Primary amino-acid sequence viewer.

MDRIIQSPGKYIQGAGAIKRLGDYLKPLAERWLVVGDKFVLGFAEEMLRKSLADAGLAAEIAPFGGECSHNEINRLRDITGNAKCTAVLGIGGGKTLDTAKALAHFMNVPVAIAPTIASTDAPCSALSVIYTDEGEFDSYLMLPRNPNMVIVDTQIVAGAPARLLAAGIGDALATWFEARACSRSGATTMAGGKCTQAALALAELCYNTLLEEGEKAMLAAEQHVVTPALERVVEANTYLSGVGFESGGLAAAHAIHNGMTAIPDAHHYYHGEKVAFGTLTQLVLENAPVDEIETVAALCHSVGLPITLAQLDIKGDIPTKMRLVAEAACAEGETIHNMPGGVDSDQVYAALLVADQYGQRFLQEWE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

3
  • 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: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:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

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

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.965
Likely same site as FPocket 1 8.0 Å 20 shared residues 77% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.857 Unusual size
Likely same site as P2Rank 1 8.0 Å 20 shared residues 77% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #2
0.546
Show in viewer
Surrounding area
All structural evidence 2 experimental · 1 predicted

Structural evidence

2 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 8K1G
X-ray A Loaded
PDB 8K1H
X-ray A Viewing
ColabFold KP13_00562
ColabFold full sequence Loaded

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
13P PDB via homolog 170.1 Da · LogP -1.34 · TPSA 104.1 Open detail RCSB PDB
1GP PDB via homolog Detail RCSB PDB
APR PDB via homolog Detail RCSB PDB
PPV PDB via homolog Detail RCSB PDB
ZINC12360002 ZINC proposed compound · Tanimoto 0.855 Detail ZINC

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 RCSB PDB Q58122 170.1 Da LogP -1.34 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)COP(=O)(O)O)O
1GP RCSB PDB Q58122 172.1 Da LogP -1.55 TPSA 107.2 ✓ Ro5 ✓ Clean C([C@@H](COP(=O)(O)O)O)O
APR RCSB PDB 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 RCSB PDB 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.