Protein target profile

VK055_1110

short chain dehydrogenase family protein

Genome: KpATCC43816 Gene: AIK79733.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GS90
Length 253
Pocket druggability 0.974
Direct ligand evidence 0 60 total records
Functional annotation 0 EC 1 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.

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 (%)
39.796 Lower values reduce human off-target concern.
Human E-value
6.47e-11
Gut microbiome similarity
1.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.04 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 0.974
Structure A0A0H3GS90
Pocket Pocket 1
P2Rank 0.955
Structure A0A0H3GS90
Pocket Pocket 1
ColabFold model
FPocket 0.649 · Pocket 4
P2Rank 0.916 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 91 / 4744 genomes with a hit
Prevalence 1.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MNNSAKIALVTGGSRGLGRATVEALAQRGVNVVLTYKTRLAEANEVVTRVEALGARAIALPFSAGEIDTFDAFVSAFQGALTELGADKFDYLVNNAGNASGMGFLNATEAEFDALYRTHVKSVFFLSQKLLPLLADGGRIVNVSSGLTRIVMANRAPYAIMKSAVETLTRYMAFELGSRGITVNCVAPVAIATDFSGGVVRDNPQVAQAVANMTALGRPGLPEDIGPMIASLLSDDHRWVNAQRIEVSGGMRI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
14 251 Pfam PF13561 Enoyl-(Acyl carrier protein) reductase
138 146 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
138 146 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
158 177 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
158 177 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
87 98 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
87 98 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
6 252 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
6 252 InterPro IPR036291 NAD(P)-binding domain superfamily
2 252 Gene3D G3DSA:3.40.50.720 -
3 251 PANTHER PTHR43639 OXIDOREDUCTASE, SHORT-CHAIN DEHYDROGENASE/REDUCTASE FAMILY (AFU_ORTHOLOGUE AFUA_5G02870)
215 235 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
215 235 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
158 177 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
7 24 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
7 24 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
87 98 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
132 148 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
132 148 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
179 196 PRINTS PR00081 Glucose/ribitol dehydrogenase family signature
179 196 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR

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 #1
0.974
Likely same site as P2Rank 1 0.8 Å 39 shared residues 95% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.955
Likely same site as FPocket 1 0.8 Å 39 shared residues 95% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.037
Show in viewer
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_A0A0H3GS90
AlphaFold DB full sequence Viewing
ColabFold VK055_1110
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.

60 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1TJ PDB via homolog 320.3 Da · LogP 2.36 · TPSA 91.7 Open detail RCSB PDB
2V4 PDB via homolog Detail RCSB PDB
CUE PDB via homolog Detail RCSB PDB
GEN PDB via homolog Detail RCSB PDB
HHF 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
1TJ RCSB PDB Q9ZGC1 320.3 Da LogP 2.36 TPSA 91.7 ✓ Ro5 Alert Cc1cc2c(c(c1)O)C3=C(C(=O)C2)C(=O)c4c(cccc4O)C3=O
2V4 RCSB PDB K0IB23 338.3 Da LogP 1.75 TPSA 111.9 ✓ Ro5 Alert C[C@]1(Cc2cc(c3c(c2C(=O)C1)C(=O)c4cccc(c4C3=O)O…
CUE RCSB PDB O93874 268.2 Da LogP 3.10 TPSA 83.8 ✓ Ro5 ✓ Clean c1cc2c(cc1O)oc-3c2C(=O)Oc4c3ccc(c4)O
GEN RCSB PDB O93874 270.2 Da LogP 2.58 TPSA 90.9 ✓ Ro5 ✓ Clean c1cc(ccc1C2=COc3cc(cc(c3C2=O)O)O)O
HHF RCSB PDB O93874 254.2 Da LogP 2.87 TPSA 70.7 ✓ Ro5 ✓ Clean c1ccc(cc1)C2=C(C(=O)c3ccc(cc3O2)O)O
KMP RCSB PDB O93874 286.2 Da LogP 2.28 TPSA 111.1 ✓ Ro5 ✓ Clean c1cc(ccc1C2=C(C(=O)c3c(cc(cc3O2)O)O)O)O
MLH RCSB PDB V5VHN7 417.3 Da LogP 4.34 TPSA 54.7 ✓ Ro5 ✓ Clean CCOC(=O)c1c2cc(c(cc2n(c1CN(C)C)c3ccccc3)Br)O
PYQ RCSB PDB Q9HFV6 173.2 Da LogP 1.52 TPSA 20.3 ✓ Ro5 ✓ Clean c1cc2c3c(c1)CCN3C(=O)CC2
QSO RCSB PDB O93874 284.3 Da LogP 2.88 TPSA 79.9 ✓ Ro5 ✓ Clean COc1ccc(cc1)C2=COc3cc(cc(c3C2=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.