Protein target profile

KP13_04437

S-(hydroxymethyl)glutathione dehydrogenase

Genome: KpKP13 Gene: AHE44310.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQL7
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Length 372
Pocket druggability 0.288
Direct ligand evidence 0 93 total records
Functional annotation 1 EC 10 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 27 structural and 16 bioactivity records.

Risks to review

Human similarity Top human hit identity: 67.273%. Microbiome similarity 177 of 4744 screened genomes (3.7%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.29.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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
Hit
Human identity (%)
67.273 Lower values reduce human off-target concern.
Human E-value
4.95e-46
Gut microbiome similarity
3.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
77.778 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.31 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.288
Structure A0A0H3GQL7
Pocket Pocket 10
P2Rank 0.937
Structure A0A0H3GQL7
Pocket Pocket 1
ColabFold model
FPocket 0.812 · Pocket 1
P2Rank 0.921 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 177 / 4744 genomes with a hit
Prevalence 3.7%

Cross-references

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

Sequence

UniProt A0A0H3GQL7

Chemistry

ChEMBL 022 ChEMBL CHEMBL4283157 ChEMBL CHEMBL4290516 ChEMBL CHEMBL4282722 ChEMBL CHEMBL4285078 ChEMBL CHEMBL4292916 ChEMBL CHEMBL4281650 ChEMBL CHEMBL4290901 ChEMBL CHEMBL4289534 ChEMBL CHEMBL4279860 ChEMBL CHEMBL4280261 ChEMBL CHEMBL4291013 ChEMBL BNF ChEMBL HPL ChEMBL CHEMBL48122 ChEMBL CHEMBL291214

Sequence

Primary amino-acid sequence viewer.

MKSRAAVAFGPGQPLKIVEIDVAPPKKGEVLVKITHTGVCHTDAFTLSGDDPEGVFPAVLGHEGGGIVVEVGEGVTSLKPGDHVIPLYTAECGECKFCKSGKTNLCQAVRATQGKGLMPDGTTRFSYNGEPIYHYMGTSTFSEYTVCAEISLAKVNPQAPLDKVCLLGCGVTTGIGAVHNTAKVKAGDSVAVFGLGGIGLAVIQGAVQAQAGRILAVDTNPDKFTLAKEMGATDFINPNDYDKPIQDVIVELTDGGVDFSFECIGNVNVMRAALECCHKGWGESVIIGVAGAGQEIKTRPFQLVTGRVWRGSAFGGVKGRSQLPGMVEDAMAGKIRLDPFITHRLPLEQINEAFDLMHEGKSIRTVIHFGDQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • 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:0006069 OBSOLETE. An ethanol metabolic process in which ethanol is converted to acetyl-CoA via acetaldehyde and acetate.
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0051903 Catalysis of the reaction: S-(hydroxymethyl)glutathione + NAD(P)+ = S-formylglutathione + NAD(P)H + H+.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004022 Catalysis of the reaction: an alcohol + NAD+ = an aldehyde or ketone + NADH + H+.
  • GO:0106322 Catalysis of the reaction: S-(hydroxymethyl)glutathione + NAD+ = S-formylglutathione + NADH + H+.
  • GO:0106321 Catalysis of the reaction: S-(hydroxymethyl)glutathione + NADP+ = S-formylglutathione + NADPH + H+.
  • GO:0080007 Catalysis of the reaction: S-nitrosoglutathione + NADH + H+ = S-(hydroxysulfenamide)glutathione + NAD+.
  • GO:0046294 The chemical reactions and pathways resulting in the breakdown of formaldehyde (methanal, H2C=O), the simplest aldehyde.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
1 187 SUPERFAMILY SSF50129 GroES-like
1 187 InterPro IPR011032 GroES-like superfamily
1 368 CDD cd08300 alcohol_DH_class_III
1 368 InterPro IPR014183 Alcohol dehydrogenase class III
61 75 ProSitePatterns PS00059 Zinc-containing alcohol dehydrogenases signature.
61 75 InterPro IPR002328 Alcohol dehydrogenase, zinc-type, conserved site
160 334 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
160 334 InterPro IPR036291 NAD(P)-binding domain superfamily
12 367 SMART SM00829 PKS_ER_names_mod
12 367 InterPro IPR020843 Polyketide synthase, enoylreductase domain
197 317 Pfam PF00107 Zinc-binding dehydrogenase
197 317 InterPro IPR013149 Alcohol dehydrogenase-like, C-terminal
174 312 FunFam G3DSA:3.40.50.720:FF:000003 S-(hydroxymethyl)glutathione dehydrogenase
2 369 NCBIfam TIGR02818 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase
2 369 InterPro IPR014183 Alcohol dehydrogenase class III
28 152 Pfam PF08240 Alcohol dehydrogenase GroES-like domain
28 152 InterPro IPR013154 Alcohol dehydrogenase-like, N-terminal
318 369 SUPERFAMILY SSF50129 GroES-like
318 369 InterPro IPR011032 GroES-like superfamily
2 367 PANTHER PTHR43880 ALCOHOL DEHYDROGENASE
174 312 Gene3D G3DSA:3.40.50.720 -
6 364 Gene3D G3DSA:3.90.180.10 -
6 189 FunFam G3DSA:3.90.180.10:FF:000001 S-(hydroxymethyl)glutathione 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 · FPocket

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

Site 1 FPocket #10
0.288
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Surrounding area
Site 2 FPocket #9
0.263
Likely same site as P2Rank 2 2.0 Å 9 shared residues 100% of smaller site
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Surrounding area
Site 3 FPocket #3
0.253
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Surrounding area
Site 4 FPocket #12
0.214
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.937
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Surrounding area
Site 2 P2Rank #2
0.162
Likely same site as FPocket 9 2.0 Å 9 shared residues 100% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.139
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Surrounding area
Site 4 P2Rank #4
0.055
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Surrounding area
Site 5 P2Rank #5
0.012
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Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

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
AlphaFold DB AF_A0A0H3GQL7
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_04437
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.

93 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 43 records from similar proteins
Structural ligands 27 0 loaded crystals
Measured bioactivity 16 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0BP PDB via homolog 156.2 Da · LogP 2.14 · TPSA 25.8 Open detail RCSB PDB
12H PDB via homolog Detail RCSB PDB
24B PDB via homolog Detail RCSB PDB
AHE PDB via homolog Detail RCSB PDB
APR PDB via homolog Detail RCSB PDB

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
0BP RCSB PDB
5VJG
P00327 156.2 Da LogP 2.14 TPSA 25.8 ✓ Ro5 ✓ Clean c1ccnc(c1)c2ccccn2
12H RCSB PDB
1M6W
P11766 216.3 Da LogP 2.96 TPSA 57.5 ✓ Ro5 ✓ Clean C(CCCCCC(=O)O)CCCCCO
24B RCSB PDB
1QV6
P00327 144.1 Da LogP 1.46 TPSA 20.2 ✓ Ro5 ✓ Clean c1cc(c(cc1F)F)CO
AHE RCSB PDB
1MC5
P11766 337.4 Da LogP -2.45 TPSA 179.1 1 viol. ✓ Clean C(CC(=O)N[C@@H](CSCO)C(=O)NCC(=O)O)[C@@H](C(=O)…
APR RCSB PDB
2FZE
P11766 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)…
CHD RCSB PDB
1EE2
P00328 408.6 Da LogP 3.45 TPSA 98.0 ✓ Ro5 ✓ Clean C[C@H](CCC(=O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C…
CND RCSB PDB
1ADB
P00327 663.4 Da LogP -3.58 TPSA 331.4 3 viol. ✓ Clean c1c(c[nH+]cc1C(=O)N)[C@H]2[C@@H]([C@@H]([C@H](O…
COD RCSB PDB
6CXX
P00327 687.6 Da LogP -1.78 TPSA 300.0 3 viol. ✓ Clean CC(C)(CO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]1[C@H]…
CXF RCSB PDB
1LDY
P00327 127.2 Da LogP 1.07 TPSA 29.1 ✓ Ro5 ✓ Clean C1CCC(CC1)NC=O
CXL RCSB PDB
1HDX
P00325 100.2 Da LogP 1.31 TPSA 20.2 ✓ Ro5 ✓ Clean C1CCC(CC1)O
DAO RCSB PDB
1MA0
P11766 200.3 Da LogP 3.99 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCCCCCC(=O)O
DFB RCSB PDB
1MG0
P00327 144.1 Da LogP 1.46 TPSA 20.2 ✓ Ro5 ✓ Clean c1cc(c(c(c1)F)F)CO
ETF RCSB PDB
1A71
P00327 100.0 Da LogP 0.54 TPSA 20.2 ✓ Ro5 ✓ Clean C(C(F)(F)F)O
FPI RCSB PDB
1LDE
P00327 113.2 Da LogP 0.63 TPSA 20.3 ✓ Ro5 ✓ Clean C1CCN(CC1)C=O
FXY RCSB PDB
1U3W
P00326 157.3 Da LogP 2.09 TPSA 29.1 ✓ Ro5 ✓ Clean CCCCCC[C@@H](C)NC=O
N2P RCSB PDB
3QJ5
P11766 102.2 Da LogP 0.07 TPSA 52.0 ✓ Ro5 ✓ Clean C(CCN)CCN
NAJ RCSB PDB
3OQ6
P00327 663.4 Da LogP -4.86 TPSA 325.2 3 viol. ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(…
NMH RCSB PDB
1P1R
P00327 143.2 Da LogP 1.70 TPSA 29.1 ✓ Ro5 ✓ Clean CCCCC[C@@H](C)NC=O
NTN RCSB PDB
7ADH
P00327 121.1 Da LogP 0.37 TPSA 62.8 ✓ Ro5 ✓ Clean c1cnccc1C(=N)N
NWH RCSB PDB
5VN1
P00327 143.2 Da LogP 1.70 TPSA 29.1 ✓ Ro5 ✓ Clean CCCCC[C@H](C)NC=O
PAD RCSB PDB
1A72
P00327 663.4 Da LogP -3.58 TPSA 331.4 3 viol. ✓ Clean c1cc([nH+]c(c1)C(=O)N)[C@H]2[C@@H]([C@@H]([C@H]…
PFB RCSB PDB
1MGO
P00327 198.1 Da LogP 1.87 TPSA 20.2 ✓ Ro5 ✓ Clean C(c1c(c(c(c(c1F)F)F)F)F)O
PHN RCSB PDB
5VJ5
P00327 180.2 Da LogP 2.78 TPSA 25.8 ✓ Ro5 ✓ Clean c1cc2ccc3cccnc3c2nc1
PYZ RCSB PDB
1DEH
P00325 194.0 Da LogP 1.01 TPSA 28.7 ✓ Ro5 ✓ Clean c1c(cn[nH]1)I
SAD RCSB PDB
1ADG
P00327 714.4 Da LogP -3.20 TPSA 318.0 3 viol. ✓ Clean c1c(nc([se]1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@…
SSB RCSB PDB
1BTO
P00327 160.3 Da LogP 1.95 TPSA 17.1 ✓ Ro5 ✓ Clean CCCC[C@H]1CC[S@](=O)C1
TAD RCSB PDB
1ADF
P00327 667.5 Da LogP -2.19 TPSA 318.0 3 viol. ✓ Clean c1c(nc(s1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@](=…

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.