KpKP13 Protein target profile

putative 3-hydroxybutyryl-CoA dehydrogenase

Accession: KP13_04974

Gene: paaH AHE44853.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWN3
Length 474
Pocket druggability (P2Rank · AlphaFold DB model) 0.789
Direct ligand evidence 0 58 total records
Functional annotation 0 EC 4 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 (%)
42.703 Lower values reduce human off-target concern.
Human E-value
2.11e-35
Gut microbiome similarity
0.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
42.294 Higher values support similarity to known essential genes.
DEG E-value
9.51e-71 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
95.03 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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) 0.789
Structure A0A0H3GWN3
Pocket Pocket 1
Druggability (FPocket) 0.438
Structure A0A0H3GWN3
Pocket Pocket 14
ColabFold model
P2Rank 0.686 · Pocket 1
FPocket 0.912 · Pocket 2
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 37 / 4744 genomes with a hit
Prevalence 0.8%

Sequence

Primary amino-acid sequence viewer.

MMTTSLVNVAVIGSGTMGAGIAEVAAAAGHPVRIFDINPKAVDLAIEGIAGRLASRVARGKLASEQADALLARLHPAHDLAALADADLVIEAASERLEVKTALFAQLAEICAPSTLLTSNTSSISITAIAAGVKKPERVAGLHFFNPAPVMKLVEVVSGLATSTEVVEQLCQCVSGWGKQPVRCRSTPGFIVNRVARPFYAEAWRALEEQVAAPEVIDAALRDGGGFPMGPLALTDLIGQDVNFAVTCSVFNAFWQDRRYLPSLLQQELALAGRLGKKSGHGVYRWPAETQPDAALPPVMMGAESVTVRSDNVTELDDVLLLETEGETALALSIKHHRPVVVYDLCASDTVVLAAAATNVPAATEKAVHYFQQQGKKVLRIADYPGLLVWRTVAMLINEALDAVQKGVASPQDVDTAMRLGVNYPHGPLAWGERLGWRRVLQLLENLQHHYGEERYRPSSLLRQKALMEKHHEQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • GO:0006631 The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
  • 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:0016616 Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
  • GO:0070403 Binding to the oxidized form, NAD, of nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
1 2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
385 466 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
385 466 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
8 185 Pfam PF02737 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain
8 185 InterPro IPR006176 3-hydroxyacyl-CoA dehydrogenase, NAD binding
298 383 Gene3D G3DSA:3.30.750.190 -
6 191 FunFam G3DSA:3.40.50.720:FF:000009 Fatty oxidation complex, alpha subunit
461 474 Coils Coil Coil
1 26 Phobius SIGNAL_PEPTIDE Signal peptide region
324 385 Pfam PF18321 3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain
324 385 InterPro IPR041040 3-hydroxybutyryl-CoA dehydrogenase reduced Rossmann-fold domain
356 465 PANTHER PTHR48075 3-HYDROXYACYL-COA DEHYDROGENASE FAMILY PROTEIN
3 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
7 29 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
8 188 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains
8 188 InterPro IPR036291 NAD(P)-binding domain superfamily
186 211 ProSitePatterns PS00067 3-hydroxyacyl-CoA dehydrogenase signature.
186 211 InterPro IPR006180 3-hydroxyacyl-CoA dehydrogenase, conserved site
188 290 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like
188 290 InterPro IPR008927 6-phosphogluconate dehydrogenase-like, C-terminal domain superfamily
2 191 Gene3D G3DSA:3.40.50.720 -
192 474 Gene3D G3DSA:1.10.1040.50 -
15 26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
189 286 Pfam PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
189 286 InterPro IPR006108 3-hydroxyacyl-CoA dehydrogenase, C-terminal
388 468 Pfam PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain
388 468 InterPro IPR006108 3-hydroxyacyl-CoA dehydrogenase, C-terminal
27 474 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.789
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.113
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.064
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.059
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.052
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #14
0.438
Show in viewer
Surrounding area
Pocket 2 FPocket #19
0.417
Show in viewer
Surrounding area
Pocket 3 FPocket #6
0.362 Unusual size
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_A0A0H3GWN3
AlphaFold DB full sequence Viewing
ColabFold KP13_04974
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3H9 PDB via homolog 877.7 Da · LogP -3.31 · TPSA 395.2 Open detail RCSB PDB
3HC PDB via homolog Detail RCSB PDB
CAA PDB via homolog Detail RCSB PDB
HSC PDB via homolog Detail RCSB PDB
N8E 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
3H9 RCSB PDB P07896 877.7 Da LogP -3.31 TPSA 395.2 3 viol. ✓ Clean CCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)…
3HC RCSB PDB Q16836 853.6 Da LogP -1.56 TPSA 383.9 3 viol. ✓ Clean CC(CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@](…
CAA RCSB PDB C4IEM5 851.6 Da LogP -1.36 TPSA 380.7 3 viol. ✓ Clean CC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P…
HSC RCSB PDB P07896 933.8 Da LogP -1.75 TPSA 395.2 3 viol. ✓ Clean CCCCCCC[C@@H](CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C…
N8E RCSB PDB P28793 350.5 Da LogP 2.42 TPSA 66.4 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCOCCO
T1G RCSB PDB P07896 863.6 Da LogP -3.85 TPSA 395.2 3 viol. ✓ Clean C[C@@H]([C@H](C)O)C(=O)SCCNC(=O)CCNC(=O)[C@@H](…
TC6 RCSB PDB P07896 859.6 Da LogP -2.51 TPSA 374.9 2 viol. ✓ Clean CCC/C=C/C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP…
ZOZ RCSB PDB P07896 935.8 Da LogP 0.98 TPSA 380.7 3 viol. ✓ Clean CCCCCCCC(=O)CC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(…

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.

Cross-references

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