Protein target profile

KP13_01311

Methylmalonate semialdehyde dehydrogenase acylating

Genome: KpKP13 Gene: AHE46625.1 iolA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GLS8
Length 501
Pocket druggability 0.542
Direct ligand evidence 0 161 total records
Functional annotation 0 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 (%)
44.094 Lower values reduce human off-target concern.
Human E-value
1.3000000000000001e-71
Gut microbiome similarity
2.7% 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
96.66 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 0.542
Structure A0A0H3GLS8
Pocket Pocket 2
P2Rank 0.819
Structure A0A0H3GLS8
Pocket Pocket 1
ColabFold model
FPocket 0.623 · Pocket 17
P2Rank 0.768 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 127 / 4744 genomes with a hit
Prevalence 2.7%

Cross-references

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

Chemistry

ChEMBL CHEMBL1607827 ChEMBL CHEMBL1498452 ChEMBL CHEMBL1200628 ChEMBL CHEMBL1542395 ChEMBL CHEMBL600769 ChEMBL CHEMBL1441067 ChEMBL CHEMBL1576608 ChEMBL CHEMBL2369196 ChEMBL CHEMBL4207222 ChEMBL CHEMBL4206892 ChEMBL CHEMBL1300462 ChEMBL CHEMBL1328800 ChEMBL CHEMBL1361393 ChEMBL CHEMBL1376427 ChEMBL CHEMBL3189457 ChEMBL CHEMBL4207514 ChEMBL CHEMBL4211904 ChEMBL CHEMBL4212671 ChEMBL CHEMBL4215704 ChEMBL CHEMBL1336893 ChEMBL CHEMBL1492006 ChEMBL CHEMBL4202680 ChEMBL CHEMBL4206272 ChEMBL CHEMBL4206606 ChEMBL CHEMBL4207617 ChEMBL CHEMBL4209722 ChEMBL CHEMBL1327135 ChEMBL CHEMBL1489143 ChEMBL CHEMBL1507858 ChEMBL CHEMBL4212891 ChEMBL CHEMBL4213848 ChEMBL CHEMBL4218688 ChEMBL CHEMBL1355293 ChEMBL CHEMBL1575066 ChEMBL CHEMBL3189647 ChEMBL CHEMBL4213604 ChEMBL CHEMBL4214724 ChEMBL CHEMBL4217115 ChEMBL CHEMBL44746 ChEMBL 3AK ChEMBL CHEMBL1330916 ChEMBL CHEMBL1509142 ChEMBL CHEMBL4207953 ChEMBL CHEMBL4210671 ChEMBL CHEMBL4205368 ChEMBL CHEMBL4205805 ChEMBL CHEMBL4215957 ChEMBL CHEMBL1415854 ChEMBL CHEMBL154580 ChEMBL CHEMBL1562420 ChEMBL CHEMBL1569332 ChEMBL CHEMBL1464178 ChEMBL CHEMBL4205051 ChEMBL CHEMBL4207423 ChEMBL CHEMBL4210811 ChEMBL CHEMBL4213304 ChEMBL CHEMBL4216229 ChEMBL ASD ChEMBL CHEMBL1200916 ChEMBL CHEMBL1406724 ChEMBL CHEMBL1556750 ChEMBL CHEMBL4202477 ChEMBL CHEMBL4204486 ChEMBL CHEMBL4204489 ChEMBL CHEMBL4214314 ChEMBL CHEMBL1347603 ChEMBL CHEMBL1392444 ChEMBL CHEMBL4203073 ChEMBL CHEMBL4208724 ChEMBL CHEMBL4213024 ChEMBL CHEMBL4214162 ChEMBL CHEMBL4216465 ChEMBL CHEMBL4209360 ChEMBL CHEMBL4214533 ChEMBL CHEMBL1324679 ChEMBL CHEMBL1471745 ChEMBL CHEMBL1514398 ChEMBL CHEMBL1526262 ChEMBL CHEMBL1539436 ChEMBL CHEMBL275742 ChEMBL CHEMBL4209616 ChEMBL CHEMBL1341327 ChEMBL CHEMBL4204849 ChEMBL CHEMBL4214428 ChEMBL CHEMBL1429775 ChEMBL CHEMBL1507462 ChEMBL CHEMBL4209231 ChEMBL WI5 ChEMBL CHEMBL1594492 ChEMBL CHEMBL4203770 ChEMBL CHEMBL4210851 ChEMBL CHEMBL4216402 ChEMBL 3XG ChEMBL CHEMBL120563 ChEMBL CHEMBL1321591 ChEMBL CHEMBL1364014 ChEMBL CHEMBL1388301 ChEMBL CHEMBL4210133 ChEMBL CHEMBL445719 ChEMBL CHEMBL567622

Sequence

Primary amino-acid sequence viewer.

MTITGNFIGGKTVISSSNETMPVYDPATGKAVREVTVSTAQEVSEAIQVARDAFDSWSRTTPLRRARVLFNFKMLLEQHVEELAGIIVSEHGKVWSDALGELTRGMEVVEFACGIPHLIKGEYSSDVGTGVDSYSLMQPLGVVAGITPFNFPAMVPMWMFPLALACGNSFVLKPPALAPTAAVRLAELLKEAGLPDGVFNVVHCSNEDAEQLYTDPRIAAVSFVGSSGVAEYIYKTASAHGKRVQAFGAAKNHAIVMPDADLDATVNAIMGGAFGSAGERCMALPVVVAVGDETADKLIARLKPLVEALKVGPGCMRGQEENEMGPVVSDTHQKKVLGYIDKGESEGAKLVVDGRKLRVPGYDAGYYVGGTLFDHVTPEMTIWREEIFGPVLGIVRAADYDSALELVNSHEFGNGSAVFTSNGHTAREFVHDVQAGMVGVNVPVPVPMAFHSFGGWKRSVFGALNVHGPDGVRFYTRMKTATVRWPAGQQTVSEFSMPTLG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

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:0016620 Catalysis of an oxidation-reduction (redox) reaction in which an aldehyde or ketone (oxo) group acts as a hydrogen or electron donor and reduces NAD or NADP.
  • GO:0004491 Catalysis of the reaction: 2-methyl-3-oxopropanoate + CoA + NAD+ = propanoyl-CoA + hydrogencarbonate + NADH + H+. Can also use malonate (3-oxopropanoate) as a substrate. The reaction occurs in two steps with the decarboxylation process preceding CoA-binding. Bicarbonate rather than CO2 is released as a final product.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
5 499 PANTHER PTHR43866 MALONATE-SEMIALDEHYDE DEHYDROGENASE
5 499 InterPro IPR010061 Methylmalonate-semialdehyde dehydrogenase
249 454 Gene3D G3DSA:3.40.309.10 Aldehyde Dehydrogenase; Chain A, domain 2
249 454 InterPro IPR016163 Aldehyde dehydrogenase, C-terminal
2 485 SUPERFAMILY SSF53720 ALDH-like
2 485 InterPro IPR016161 Aldehyde/histidinol dehydrogenase
23 462 Gene3D G3DSA:3.40.605.10 Aldehyde Dehydrogenase; Chain A, domain 1
23 462 InterPro IPR016162 Aldehyde dehydrogenase, N-terminal
249 454 FunFam G3DSA:3.40.309.10:FF:000002 Methylmalonate-semialdehyde dehydrogenase (Acylating)
4 485 CDD cd07085 ALDH_F6_MMSDH
4 485 InterPro IPR010061 Methylmalonate-semialdehyde dehydrogenase
15 480 Pfam PF00171 Aldehyde dehydrogenase family
15 480 InterPro IPR015590 Aldehyde dehydrogenase domain
8 255 FunFam G3DSA:3.40.605.10:FF:000003 Methylmalonate-semialdehyde dehydrogenase [acylating]
6 485 NCBIfam TIGR01722 CoA-acylating methylmalonate-semialdehyde dehydrogenase
6 485 InterPro IPR010061 Methylmalonate-semialdehyde 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 #2
0.542
Likely same site as P2Rank 2 2.4 Å 12 shared residues 80% of smaller site
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Surrounding area
Site 2 FPocket #8
0.451
Likely same site as P2Rank 1 4.3 Å 12 shared residues 80% of smaller site
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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
0.819
Likely same site as FPocket 8 4.3 Å 12 shared residues 80% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.534
Likely same site as FPocket 2 2.4 Å 12 shared residues 80% of smaller site
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Surrounding area
Site 3 P2Rank #3
0.124
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.015
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.008
Likely same site as FPocket 8 7.7 Å 4 shared residues 50% of smaller site
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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_A0A0H3GLS8
AlphaFold DB full sequence Viewing
ColabFold KP13_01311
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.

161 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 111 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
6ZU PDB via homolog 344.4 Da · LogP 3.03 · TPSA 73.6 Open detail RCSB PDB
7PE PDB via homolog Detail RCSB PDB
A5Y PDB via homolog Detail RCSB PDB
DTT PDB via homolog Detail RCSB PDB
K9P 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
6ZU RCSB PDB P00352 344.4 Da LogP 3.03 TPSA 73.6 ✓ Ro5 ✓ Clean CC1=C(C(=O)Oc2c1ccc(c2)OS(=O)(=O)C)Cc3ccccc3
7PE RCSB PDB Q9HTJ1 310.4 Da LogP 0.10 TPSA 75.6 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCO
A5Y RCSB PDB P00352 408.5 Da LogP 3.58 TPSA 61.9 ✓ Ro5 ✓ Clean c1ccc(cc1)N2C(=O)c3cn(nc3N=C2SCc4cccc(c4)F)C5CO…
DTT RCSB PDB Q9HTJ1 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
K9P RCSB PDB P00352 297.4 Da LogP 4.58 TPSA 40.5 ✓ Ro5 ✓ Clean CCCCCC(=O)N1C[C@H](c2c1cc(c3c2cccc3)O)C
M39 RCSB PDB P00352 366.4 Da LogP 3.85 TPSA 63.6 ✓ Ro5 ✓ Clean Cc1ccccc1N2C(=O)c3c[nH]nc3N=C2SCc4cccc(c4)F
PE4 RCSB PDB Q9HTJ1 354.4 Da LogP 0.11 TPSA 84.8 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCO
SIN RCSB PDB Q3JLL8 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
TAP RCSB PDB P28037 759.5 Da LogP -3.00 TPSA 350.6 3 viol. ✓ Clean c1cc(c[n+](c1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P…
TOE RCSB PDB Q9HTJ1 164.2 Da LogP -0.34 TPSA 47.9 ✓ Ro5 ✓ Clean COCCOCCOCCO
TXE RCSB PDB P00352 667.5 Da LogP -2.95 TPSA 317.6 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.