Protein target profile

KP13_03396

2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase

Genome: KpKP13 Gene: AHE45774.1 entA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GPR7
Length 251
Pocket druggability 0.876
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 3 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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 (%)
34.058 Lower values reduce human off-target concern.
Human E-value
1.58e-15
Gut microbiome similarity
1.8% 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.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.35 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 0.876
Structure A0A0H3GPR7
Pocket Pocket 1
P2Rank 0.914
Structure A0A0H3GPR7
Pocket Pocket 1
ColabFold model
FPocket 0.892 · Pocket 1
P2Rank 0.883 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 84 / 4744 genomes with a hit
Prevalence 1.8%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MAALDFRGQTVWVTGAGKGIGYATALAFVEAGANVTGFDLAFDGESYPFATETLDVADADQVREACSRLLANTERLDVLVNAAGILRMGATDQLSAEDWQQTFAVNVGGAFNLFQQTMAQFRRQRGGAIVTVASDAAHTPRIGMSAYGASKAALKSLALTVGLELAGSGVRCNLVSPGSTDTDMQRTLWVSDDAEQQRIRGFGEQFKLGIPLGKIARPQEIANTILFLASSHASHITLQDIVVDGGSTLGA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

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:0019290 The chemical reactions and pathways resulting in the formation of siderophores, low molecular weight Fe(III)-chelating substances made by aerobic or facultatively anaerobic bacteria, especially when growing under iron deficient conditions. The complexes of Fe(3+)-siderophores have very high stability constants and are taken up by specific transport systems by microorganisms; the subsequent release of iron requires enzymatic action.
  • GO:0008667 Catalysis of the reaction: (2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoate + NAD+ = 2,3-dihydroxybenzoate + H+ + NADH.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
1 249 FunFam G3DSA:3.40.50.720:FF:000160 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
9 180 SMART SM00822 This enzymatic domain is part of bacterial polyketide synthases and catalyses the first step in the reductive modification of the beta-carbonyl centres in the growing polyketide chain. It uses NADPH to reduce the keto group to a hydroxy group.
15 248 Pfam PF13561 Enoyl-(Acyl carrier protein) reductase
3 248 PANTHER PTHR24321 DEHYDROGENASES, SHORT CHAIN
2 250 Gene3D G3DSA:3.40.50.720 -
134 162 ProSitePatterns PS00061 Short-chain dehydrogenases/reductases family signature.
134 162 InterPro IPR020904 Short-chain dehydrogenase/reductase, conserved site
127 135 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
127 135 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
74 85 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
74 85 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
147 166 PRINTS PR00080 Short-chain dehydrogenase/reductase (SDR) superfamily signature
147 166 InterPro IPR002347 Short-chain dehydrogenase/reductase SDR
4 248 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
4 248 InterPro IPR036291 NAD(P)-binding domain superfamily
11 251 CDD cd05331 DH-DHB-DH_SDR_c
11 251 InterPro IPR003560 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
15 32 PRINTS PR01397 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
15 32 InterPro IPR003560 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
162 185 PRINTS PR01397 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
162 185 InterPro IPR003560 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
201 220 PRINTS PR01397 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
201 220 InterPro IPR003560 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
97 117 PRINTS PR01397 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
97 117 InterPro IPR003560 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
77 94 PRINTS PR01397 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
77 94 InterPro IPR003560 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
227 246 PRINTS PR01397 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase signature
227 246 InterPro IPR003560 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
11 250 NCBIfam TIGR04316 2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase
11 250 InterPro IPR003560 2,3-dihydro-2,3-dihydroxybenzoate 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 #1
0.876
Likely same site as P2Rank 1 5.2 Å 34 shared residues 87% 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
0.914
Likely same site as FPocket 1 5.2 Å 34 shared residues 87% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.013
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.011
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_A0A0H3GPR7
AlphaFold DB full sequence Viewing
ColabFold KP13_03396
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
A6O PDB via homolog 314.4 Da · LogP 3.93 · TPSA 46.5 Open detail RCSB PDB
BUO PDB via homolog Detail RCSB PDB
ISN PDB via homolog Detail RCSB PDB
RM4 PDB via homolog Detail RCSB PDB
TAM 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
A6O RCSB PDB C0IR58 314.4 Da LogP 3.93 TPSA 46.5 ✓ Ro5 ✓ Clean CC[C@]1([C@H](CCC1=O)O)C/C=C/2\CCCc3c2ccc(c3)OC
BUO RCSB PDB G5EGA6 86.1 Da LogP 0.16 TPSA 34.1 ✓ Ro5 Alert CC(=O)C(=O)C
ISN RCSB PDB G5EGA6 147.1 Da LogP 0.82 TPSA 46.2 ✓ Ro5 ✓ Clean c1ccc2c(c1)C(=O)C(=O)N2
RM4 RCSB PDB C1DMX5 164.2 Da LogP -2.19 TPSA 90.2 ✓ Ro5 ✓ Clean C[C@H]1[C@@H]([C@H]([C@H]([C@H](O1)O)O)O)O
TAM RCSB PDB C0IR58 163.2 Da LogP -1.17 TPSA 86.7 ✓ Ro5 ✓ Clean C(CO)C(CCO)(CCO)N
TLA RCSB PDB B4EEX4 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
TNE RCSB PDB Q19774 139.2 Da LogP 0.81 TPSA 20.3 ✓ Ro5 ✓ Clean CN1[C@H]2CC[C@@H]1CC(=O)C2

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.