KpKP13 Protein target profile

Malonate decarboxylase subunit beta

Accession: KP13_01177

Gene: AHE44760.1 mdcD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSG2
Length 277
Pocket druggability (P2Rank · AlphaFold DB model) 0.066
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 6 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 (%)
28.636 Lower values reduce human off-target concern.
Human E-value
1.06e-07
Gut microbiome similarity
1.7% 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.

Structure confidence

ColabFold pLDDT
96.05 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) 0.066
Structure A0A0H3GSG2
Pocket Pocket 1
Druggability (FPocket) 0.771
Structure A0A0H3GSG2
Pocket Pocket 4
ColabFold model
P2Rank 0.064 · Pocket 1
FPocket 0.785 · Pocket 10
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 82 / 4744 genomes with a hit
Prevalence 1.7%

Sequence

Primary amino-acid sequence viewer.

MRNDRSFIELRARERAHALLDDGSYRELLDPFDGIMSPWLGAQGIVPQSDDGMVVAKGTINGQPAVVIAIEGTFQGGSMGEVSGAKMAAALELAAEDNRNGIPTQAVLCLETGGVRLQEANLGLAAIADIHAAIVDLRRYTPVVGIIAGTVGCFGGMSIAAALCSYLIVTREARLGLNGPQVIEQEAGIEEYDSRNRPFIWSMTGGEIRAASGLVDALVNDGVNAVKTAMNEAIAKGVPVQHRSDNYDDYLRRLSQFDTRQQADTAQIKQLFAREDK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

6
  • GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
  • GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0003989 Catalysis of the reaction: ATP + acetyl-CoA + HCO3- = ADP + phosphate + malonyl-CoA.
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • GO:0006633 The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
  • GO:2001295 The chemical reactions and pathways resulting in the formation of malonyl-CoA, the S-malonyl derivative of coenzyme A.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
143 169 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
1 242 ProSiteProfiles PS50980 Acetyl-coenzyme A (CoA) carboxyltransferase N-terminal domain profile.
1 242 InterPro IPR011762 Acetyl-coenzyme A carboxyltransferase, N-terminal
5 275 NCBIfam TIGR03133 biotin-independent malonate decarboxylase subunit beta
5 275 InterPro IPR017556 Biotin-independent malonate decarboxylase, beta subunit
170 277 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 142 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
147 169 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
5 222 SUPERFAMILY SSF52096 ClpP/crotonase
5 222 InterPro IPR029045 ClpP/crotonase-like domain superfamily
48 220 PANTHER PTHR42995 ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT BETA, CHLOROPLASTIC
12 231 Pfam PF01039 Carboxyl transferase domain
12 231 InterPro IPR034733 Acetyl-CoA carboxylase
3 231 Gene3D G3DSA:3.90.226.10 -

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.066
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Surrounding area
Pocket 2 P2Rank #2
0.051
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Surrounding area
Pocket 3 P2Rank #3
0.048
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Surrounding area
Pocket 4 P2Rank #4
0.016
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Surrounding area
Pocket 5 P2Rank #5
0.014
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.771
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Surrounding area
Pocket 2 FPocket #10
0.727
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Surrounding area
Pocket 3 FPocket #5
0.201
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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_A0A0H3GSG2
AlphaFold DB full sequence Viewing
ColabFold KP13_01177
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1VU PDB via homolog 823.6 Da · LogP -0.93 · TPSA 363.6 Open detail RCSB PDB
BTI PDB via homolog Detail RCSB PDB
DXX PDB via homolog Detail RCSB PDB
HXC PDB via homolog Detail RCSB PDB
MCA 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
1VU RCSB PDB Q9X4K7 823.6 Da LogP -0.93 TPSA 363.6 3 viol. ✓ Clean CCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O…
BTI RCSB PDB C5AP75 228.3 Da LogP 0.91 TPSA 58.2 ✓ Ro5 ✓ Clean C1[C@H]2[C@@H]([C@@H](S1)CCCCC=O)NC(=O)N2
DXX RCSB PDB Q8GBW6 118.1 Da LogP -0.21 TPSA 74.6 ✓ Ro5 ✓ Clean CC(C(=O)O)C(=O)O
HXC RCSB PDB A0ACI9 865.7 Da LogP 0.25 TPSA 363.6 3 viol. ✓ Clean CCCCCC(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO[P@@…
MCA RCSB PDB Q8GBW6 867.6 Da LogP -1.61 TPSA 400.9 3 viol. ✓ Clean C[C@H](C(=O)O)C(=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.