KpKP13 Protein target profile

2,3-dihydroxybenzoic acid decarboxylase

Accession: KP13_31623

Gene: AHE47008.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GH28

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Length 332

Pocket druggability (P2Rank · AlphaFold DB model) 0.867

Direct ligand evidence 0 59 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.

Main supporting evidence

Moderate predicted binding pocket FPocket selected-pocket score 0.56. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.87. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 9 structural and 0 bioactivity records.

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%): 25.09 Lower values reduce human off-target concern.
Human E-value: 1.43e-15
Gut microbiome similarity: 0.2% 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: 96.72 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) 0.867

Structure A0A0H3GH28

Pocket Pocket 1

Druggability (FPocket) 0.556

Structure A0A0H3GH28

Pocket Pocket 2

ColabFold model

P2Rank 0.768 · Pocket 1

FPocket 0.592 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 10 / 4744 genomes with a hit

Prevalence 0.2%

Sequence

Primary amino-acid sequence viewer.

MRGKIALEEHVSTPENNRLWDSSGEAGRNGTEYMKDVERRLLDRSIQLEEMAQRHIDHVILSLTSPGAQSILDKAKAVSFARETNDFIVENYVKPNPDKFSAFATLALQNPEAAAEELERAVKKLGMKGALINGYTNVKDSEHGLYLDDESMLVFWDKVNELNVPVYLHPREPLEGPARGIYTGYESLIGSAWGFAQETAVHAIRLMMSGLFDRYPNLNLVLGHLGEGLVHMLPRTQHRLYRQRFGCGLGKAEKPLMHYLQNNFIVTTSGHFNTHSLNNAIEVMGADRVMFSVDYPYEDIHQACDWFDPLELEAGLKEKIAWGNASRVFNIK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0016831 Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0019748 The chemical reactions and pathways resulting in many of the chemical changes of compounds that are not necessarily required for growth and maintenance of cells, and are often unique to a taxon. In multicellular organisms secondary metabolism is generally carried out in specific cell types, and may be useful for the organism as a whole. In unicellular organisms, secondary metabolism is often used for the production of antibiotics or for the utilization and acquisition of unusual nutrients.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

7 records

Show feature table

Start	End	DB	Term	Name
2	330	PANTHER	PTHR21240	2-AMINO-3-CARBOXYLMUCONATE-6-SEMIALDEHYDE DECARBOXYLASE
2	330	InterPro	IPR032465	2-amino-3-carboxymuconate-6-semialdehyde decarboxylase
23	331	Pfam	PF04909	Amidohydrolase
23	331	InterPro	IPR006680	Amidohydrolase-related
1	332	Gene3D	G3DSA:3.20.20.140	-
16	331	SUPERFAMILY	SSF51556	Metallo-dependent hydrolases
16	331	InterPro	IPR032466	Metal-dependent hydrolase

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

0.867

Likely same site as FPocket 2 5.1 Å 22 shared residues 79% of smaller site

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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 #2

0.556 Unusual size

Likely same site as P2Rank 1 5.1 Å 22 shared residues 79% of smaller site

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Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.768

Likely same site as FPocket 1 1.4 Å 26 shared residues 93% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.319

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Surrounding area

Pocket 3 P2Rank #3

0.223

Likely same site as FPocket 18 6.9 Å 7 shared residues 64% of smaller site

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Surrounding area

Pocket 4 P2Rank #4

0.03

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Surrounding area

Pocket 5 P2Rank #5

0.011

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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 #1

0.592 Unusual size

Likely same site as P2Rank 1 1.4 Å 26 shared residues 93% of smaller site

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Surrounding area

Pocket 2 FPocket #3

0.466

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Surrounding area

Pocket 3 FPocket #18

0.4 Unusual size

Likely same site as P2Rank 3 6.9 Å 7 shared residues 64% 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_A0A0H3GH28	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_31623	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.

59 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 9 records from similar proteins

Structural ligands 9 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

1DF PDB via homolog 213.1 Da · LogP 1.01 · TPSA 109.9 Open detail RCSB PDB

1WB PDB via homolog Detail RCSB PDB

23A PDB via homolog Detail RCSB PDB

38L PDB via homolog Detail RCSB PDB

CAQ PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
1DF RCSB PDB	4NG3	Q8RJ47	213.1 Da LogP 1.01 TPSA 109.9	✓ Ro5	✓ Clean	`COc1cc(cc(c1O)[N+](=O)[O-])C(=O)O`
1WB RCSB PDB	4NI8	Q8RJ47	196.2 Da LogP 1.09 TPSA 83.8	✓ Ro5	✓ Clean	`COc1cc(cc(c1)C(=O)O)C(=O)O`
23A RCSB PDB	2DVX	Q60GU1	138.1 Da LogP 0.91 TPSA 57.5	✓ Ro5	Alert	`c1cc(c(c(c1)O)O)C=O`
38L RCSB PDB	4QRO	Q12BV1	155.1 Da LogP 1.01 TPSA 83.6	✓ Ro5	✓ Clean	`c1cc(c(c(c1)O)[N+](=O)[O-])O`
CAQ RCSB PDB	7BP1	N1S495	110.1 Da LogP 1.10 TPSA 40.5	✓ Ro5	Alert	`c1ccc(c(c1)O)O`
GRE RCSB PDB	2DVU	Q60GU1	154.1 Da LogP 0.80 TPSA 77.8	✓ Ro5	✓ Clean	`c1cc(c(c(c1)O)C(=O)O)O`
GTQ RCSB PDB	7BPC	N1S495	154.1 Da LogP 0.80 TPSA 77.8	✓ Ro5	✓ Clean	`c1cc(c(cc1O)C(=O)O)O`
SAL RCSB PDB	6JQX	P0CT50	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1ccc(c(c1)C(=O)O)O`
VNL RCSB PDB	4L6D	Q8RJ47	167.1 Da LogP -0.24 TPSA 69.6	✓ Ro5	✓ Clean	`COc1cc(ccc1O)C(=O)[O-]`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC37011453 ZINC	1.000	213.1 Da LogP 1.01 TPSA 109.9	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc([N+](=O)[O-])c1O`
ZINC2513856 ZINC	0.800	210.2 Da LogP 1.18 TPSA 72.8	✓ Ro5	✓ Clean	`COC(=O)c1cc(OC)cc(C(=O)O)c1`
ZINC1635818 ZINC	0.771	211.2 Da LogP 1.51 TPSA 89.7	✓ Ro5	✓ Clean	`COc1cc(C(C)=O)cc([N+](=O)[O-])c1O`
ZINC43828194 ZINC	0.750	227.2 Da LogP 1.10 TPSA 98.9	✓ Ro5	✓ Clean	`COC(=O)c1cc(OC)c(O)c([N+](=O)[O-])c1`
ZINC6667014 ZINC	0.743	227.2 Da LogP 1.31 TPSA 98.9	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc([N+](=O)[O-])c1OC`
ZINC393525 ZINC	0.731	231.0 Da LogP 2.16 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(Br)cc(C(=O)O)c1`
ZINC91691843 ZINC	0.731	278.0 Da LogP 2.00 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(I)cc(C(=O)O)c1`
ZINC43386544 ZINC	0.722	211.2 Da LogP 1.61 TPSA 89.7	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc([N+](=O)[O-])c1C`
ZINC16125291 ZINC	0.708	218.0 Da LogP 2.06 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1c(O)cccc1Br`
ZINC169278691 ZINC	0.703	231.6 Da LogP 1.95 TPSA 89.7	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc([N+](=O)[O-])c1Cl`
ZINC199784029 ZINC	0.703	212.2 Da LogP 0.88 TPSA 115.7	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc([N+](=O)[O-])c1N`
ZINC2055151981 ZINC	0.703	323.0 Da LogP 1.91 TPSA 89.7	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc([N+](=O)[O-])c1I`
ZINC38327801 ZINC	0.696	242.2 Da LogP 2.39 TPSA 74.6	✓ Ro5	✓ Clean	`O=Cc1cccc(-c2cccc(C=O)c2O)c1O`
ZINC2004507 ZINC	0.688	228.1 Da LogP 0.91 TPSA 143.8	✓ Ro5	✓ Clean	`O=C(O)c1cc([N+](=O)[O-])c(O)c([N+](=O)[O-])c1`
ZINC107267830 ZINC	0.679	202.2 Da LogP 2.33 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc(C(F)F)c1`
ZINC16159041 ZINC	0.679	220.1 Da LogP 2.41 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc(C(F)(F)F)c1`
ZINC1670022 ZINC	0.679	258.2 Da LogP 2.03 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1cc(O)ccc1O`
ZINC85476716 ZINC	0.679	236.1 Da LogP 2.29 TPSA 55.8	✓ Ro5	✓ Clean	`COc1cc(OC(F)(F)F)cc(C(=O)O)c1`
ZINC1595860 ZINC	0.677	316.3 Da LogP 2.48 TPSA 82.1	✓ Ro5	Alert	`COc1cc(C(=O)C(=O)c2ccc(OC)c(OC)c2)ccc1O`
ZINC34572642 ZINC	0.667	274.2 Da LogP 2.16 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccc(O)c(C(=O)O)c2)ccc1O`
ZINC12411559 ZINC	0.659	268.3 Da LogP 1.79 TPSA 92.9	✓ Ro5	✓ Clean	`CCN(CC)C(=O)c1cc(OC)c(O)c([N+](=O)[O-])c1`
ZINC77303491 ZINC	0.659	287.3 Da LogP 2.85 TPSA 89.7	✓ Ro5	✓ Clean	`COc1cc(C(=O)c2ccc(C)cc2)cc([N+](=O)[O-])c1O`
ZINC1583337 ZINC	0.657	242.1 Da LogP 1.21 TPSA 132.8	✓ Ro5	✓ Clean	`COc1c([N+](=O)[O-])cc(C(=O)O)cc1[N+](=O)[O-]`
ZINC103291148 ZINC	0.656	356.4 Da LogP 3.52 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(C(=O)/C(C)=C(/C)C(=O)c2ccc(O)c(OC)c2)ccc…`
ZINC2559238 ZINC	0.655	209.2 Da LogP 1.35 TPSA 75.6	✓ Ro5	✓ Clean	`COc1cc(NC(C)=O)cc(C(=O)O)c1`
ZINC47211920 ZINC	0.655	228.2 Da LogP 3.06 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc(-c2ccccc2)c1`
ZINC65349987 ZINC	0.655	258.3 Da LogP 3.07 TPSA 55.8	✓ Ro5	✓ Clean	`COc1ccc(-c2cc(OC)cc(C(=O)O)c2)cc1`
ZINC65350662 ZINC	0.655	272.3 Da LogP 2.76 TPSA 83.8	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc(-c2ccc(C(=O)O)cc2)c1`
ZINC15121898 ZINC	0.652	346.2 Da LogP 2.27 TPSA 158.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(Oc2cc(C(=O)O)cc(C(=O)O)c2)cc(C(=O)O)…`
ZINC12471629 ZINC	0.640	201.0 Da LogP 1.97 TPSA 37.3	✓ Ro5	✓ Clean	`O=Cc1cccc(Br)c1O`
ZINC2048532872 ZINC	0.640	350.3 Da LogP 3.83 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccc(-c3ccc(O)c(C(=O)O)c3)cc2)ccc1O`
ZINC403469 ZINC	0.640	224.2 Da LogP 1.27 TPSA 61.8	✓ Ro5	✓ Clean	`COC(=O)c1cc(OC)cc(C(=O)OC)c1`
ZINC82374681 ZINC	0.640	210.2 Da LogP 0.97 TPSA 72.8	✓ Ro5	✓ Clean	`COc1cc(OC)cc(C(=O)C(=O)O)c1`
ZINC95932450 ZINC	0.640	248.0 Da LogP 1.81 TPSA 37.3	✓ Ro5	✓ Clean	`O=Cc1cccc(I)c1O`
ZINC4343573 ZINC	0.639	214.1 Da LogP 1.22 TPSA 115.7	✓ Ro5	✓ Clean	`COc1cc([N+](=O)[O-])cc([N+](=O)[O-])c1O`
ZINC308929387 ZINC	0.633	231.2 Da LogP 0.04 TPSA 106.7	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc(S(N)(=O)=O)c1`
ZINC65349492 ZINC	0.633	242.3 Da LogP 3.37 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc(-c2ccc(C)cc2)c1`
ZINC65350398 ZINC	0.633	264.2 Da LogP 3.34 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc(-c2cc(F)cc(F)c2)c1`
ZINC65354348 ZINC	0.633	297.1 Da LogP 4.37 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)O)cc(-c2cc(Cl)cc(Cl)c2)c1`
ZINC149139339 ZINC	0.630	218.2 Da LogP -0.05 TPSA 123.5	✓ Ro5	✓ Clean	`NS(=O)(=O)c1cccc(O)c1[N+](=O)[O-]`
ZINC63110848 ZINC	0.630	207.1 Da LogP 2.32 TPSA 63.4	✓ Ro5	✓ Clean	`O=[N+]([O-])c1c(O)cccc1C(F)(F)F`
ZINC2048532699 ZINC	0.625	482.4 Da LogP 3.76 TPSA 205.0	✓ Ro5	✓ Clean	`O=C(O)c1cc(Oc2cc(C(=O)O)cc(C(=O)O)c2)cc(Oc2cc(C…`
ZINC34566642 ZINC	0.625	227.2 Da LogP 0.94 TPSA 109.9	✓ Ro5	✓ Clean	`COc1cc(CC(=O)O)cc([N+](=O)[O-])c1O`
ZINC426571571 ZINC	0.625	253.3 Da LogP 0.77 TPSA 84.9	✓ Ro5	✓ Clean	`COCCNC(=O)c1cc(OC)cc(C(=O)O)c1`
ZINC90525715 ZINC	0.625	302.3 Da LogP 2.95 TPSA 54.0	✓ Ro5	✓ Clean	`COc1cc(OC)cc(C(=O)c2cc(OC)cc(OC)c2)c1`
ZINC95080312 ZINC	0.622	248.0 Da LogP 2.07 TPSA 72.6	✓ Ro5	✓ Clean	`COc1cc(Br)cc([N+](=O)[O-])c1O`
ZINC1747330 ZINC	0.618	362.3 Da LogP 2.13 TPSA 111.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)OCCOC(=O)c2ccc(O)c(OC)c2)ccc1O`
ZINC38237511 ZINC	0.618	242.3 Da LogP 2.94 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)c2ccc(C)cc2)ccc1O`
ZINC154623 ZINC	0.615	217.0 Da LogP 1.85 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(Br)ccc1O`
ZINC156387 ZINC	0.615	264.0 Da LogP 1.70 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1cc(I)ccc1O`

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.

Sequence

UniProt A0A0H3GH28