Protein target profile

KP13_04940

N-methyl-L-tryptophan oxidase

Genome: KpKP13 Gene: AHE45302.1 solA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRF7

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Length 372

Pocket druggability 1

Direct ligand evidence 0 61 total records

Functional annotation 1 EC 5 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.

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 1.00, P2Rank 0.99). Use the 3D pocket comparison to verify whether they identify the same site. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 1.00. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.99. Review the complete evidence below

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 (%): 30.026 Lower values reduce human off-target concern.
Human E-value: 2.52e-44
Gut microbiome similarity: 1.9% 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: 96.93 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 1

Structure A0A0H3GRF7

Pocket Pocket 1

P2Rank 0.989

Structure A0A0H3GRF7

Pocket Pocket 1

ColabFold model

FPocket 0.998 · Pocket 1

P2Rank 0.985 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 91 / 4744 genomes with a hit

Prevalence 1.9%

Cross-references

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

Sequence

UniProt A0A0H3GRF7

Sequence

Primary amino-acid sequence viewer.

MQYDLIIIGSGSVGAAAGYYARRAGLNVLMTDAHQPPHQEGSHHGSSRLIRHAYGEGEKYVPLVLRAQQLWDELAEISGEAVFERTGVINLGPASSAFLANVAASARAFQLEVEELDAQAVMQRWPEIRLPDDYRAIFEPASGVLRSELAVETWIRLAREAGCAQLFNCPVSAIHHHADGITIDTLDGEYHGKKLLVSAGTWVTRLLPDLPIQPVRKVFAWYQADGRYSSKNHFPAFTGELPNGDQYYGFPAEDNELKIGKHNGGQPISTPQERVAFGAVASDGSESFPFLRNVLPGIGGCLHGASCTYDNTVDEDFIIDTLPGRPDTLLITGLSGHGFKFAPVLGEIASQFAQGEASSFNLAPFSLARFNA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1.5.3.-

Gene Ontology (GO)

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:0050131 Catalysis of the reaction: an N-methyl-L-amino acid + H2O + O2 = an L-amino acid + formaldehyde + H2O2.
GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008115 Catalysis of the reaction: H2O + O2 + sarcosine = formaldehyde + glycine + H2O2.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

12 records

Show feature table

Start	End	DB	Term	Name
1	371	Hamap	MF_00515	N-methyl-L-tryptophan oxidase [solA].
1	371	InterPro	IPR023493	N-methyl-L-tryptophan oxidase MTOX
4	350	Pfam	PF01266	FAD dependent oxidoreductase
4	350	InterPro	IPR006076	FAD dependent oxidoreductase
2	370	SUPERFAMILY	SSF51905	FAD/NAD(P)-binding domain
2	370	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily
2	371	PANTHER	PTHR10961	PEROXISOMAL SARCOSINE OXIDASE
2	371	InterPro	IPR045170	MTOX family
59	313	Gene3D	G3DSA:3.30.9.10	-
212	312	SUPERFAMILY	SSF54373	FAD-linked reductases, C-terminal domain
4	356	Gene3D	G3DSA:3.50.50.60	-
4	356	InterPro	IPR036188	FAD/NAD(P)-binding domain superfamily

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

1.0

Likely same site as P2Rank 1 1.0 Å 50 shared residues 94% of smaller site

Unusual size

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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

0.989

Likely same site as FPocket 1 1.0 Å 50 shared residues 94% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.056

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Surrounding area

Site 3 P2Rank #3

0.028

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Surrounding area

Site 4 P2Rank #4

0.014

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Surrounding area

Site 5 P2Rank #5

0.008

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Surrounding area

Residue sets

UniProt: Binding site:4-34

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.985

Likely same site as FPocket 1 0.3 Å 48 shared residues 96% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.114

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Surrounding area

Site 3 P2Rank #3

0.1

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Surrounding area

Site 4 P2Rank #4

0.012

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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_A0A0H3GRF7	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_04940	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.

61 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 11 records from similar proteins

Structural ligands 11 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

6PC PDB via homolog 123.1 Da · LogP 0.78 · TPSA 50.2 Open detail RCSB PDB

BEZ PDB via homolog Detail RCSB PDB

DMG PDB via homolog Detail RCSB PDB

FCG PDB via homolog Detail RCSB PDB

FOA 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
6PC RCSB PDB	2OLN	Q9X9P9	123.1 Da LogP 0.78 TPSA 50.2	✓ Ro5	✓ Clean	`c1ccnc(c1)C(=O)O`
BEZ RCSB PDB	2Q6U	Q9X9P9	122.1 Da LogP 1.38 TPSA 37.3	✓ Ro5	✓ Clean	`c1ccc(cc1)C(=O)O`
DMG RCSB PDB	1EL5	P40859	103.1 Da LogP -0.37 TPSA 40.5	✓ Ro5	✓ Clean	`CN(C)CC(=O)O`
FCG RCSB PDB	2A89	P40859	847.7 Da LogP -2.89 TPSA 370.4	3 viol.	✓ Clean	`Cc1cc2c(cc1C)[N@]3[C@@H](CC[C@@]34C(N2C[C@@H]([…`
FOA RCSB PDB	2GF3	P40859	112.1 Da LogP 0.98 TPSA 50.4	✓ Ro5	✓ Clean	`c1cc(oc1)C(=O)O`
MSF RCSB PDB	1EL8	P40859	152.0 Da LogP -1.09 TPSA 40.1	✓ Ro5	✓ Clean	`C[Se]CC(=O)[O-]`
MTD RCSB PDB	1EL7	P40859	200.7 Da LogP -1.09 TPSA 40.1	✓ Ro5	✓ Clean	`C[Te]CC(=O)[O-]`
MTG RCSB PDB	1EL9	P40859	105.1 Da LogP -0.90 TPSA 40.1	✓ Ro5	✓ Clean	`CSCC(=O)[O-]`
PYC RCSB PDB	1ELI	P40859	110.1 Da LogP -0.62 TPSA 55.9	✓ Ro5	✓ Clean	`c1cc([nH]c1)C(=O)[O-]`
SAR RCSB PDB	3QSE	P40859	89.1 Da LogP -0.71 TPSA 49.3	✓ Ro5	✓ Clean	`CNCC(=O)O`
TE RCSB PDB	1EL7	P40859	129.6 Da LogP -0.92 TPSA 0.0	✓ Ro5	✓ Clean	`[TeH2]`

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
ZINC3269660 ZINC	0.824	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC2504355 ZINC	0.778	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC1747039 ZINC	0.696	212.2 Da LogP 1.54 TPSA 59.9	✓ Ro5	Alert	`O=C(C(=O)c1ccccn1)c1ccccn1`
ZINC1672966 ZINC	0.688	210.2 Da LogP 2.75 TPSA 34.1	✓ Ro5	Alert	`O=C(C(=O)c1ccccc1)c1ccccc1`
ZINC34057267 ZINC	0.684	274.3 Da LogP 4.72 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccccc3)cc2)cc1`
ZINC85394426 ZINC	0.667	206.2 Da LogP 1.80 TPSA 80.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccco2)o1`
ZINC1698355 ZINC	0.654	211.2 Da LogP 2.15 TPSA 47.0	✓ Ro5	Alert	`O=C(C(=O)c1ccccn1)c1ccccc1`
ZINC114185151 ZINC	0.647	298.2 Da LogP 2.15 TPSA 108.7	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC1590838 ZINC	0.647	342.4 Da LogP 3.82 TPSA 68.3	✓ Ro5	Alert	`O=C(C(=O)c1ccc(C(=O)C(=O)c2ccccc2)cc1)c1ccccc1`
ZINC1572316 ZINC	0.643	227.2 Da LogP 2.01 TPSA 67.3	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccccn1`
ZINC100005308 ZINC	0.640	226.2 Da LogP 1.93 TPSA 59.9	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccccn1)c1ccccn1`
ZINC35653976 ZINC	0.621	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2ccccn2)n1`
ZINC2168275 ZINC	0.619	203.2 Da LogP -2.48 TPSA 107.5	✓ Ro5	✓ Clean	`CNCC(=O)NCC(=O)NCC(=O)O`
ZINC145462956 ZINC	0.615	240.3 Da LogP 2.32 TPSA 59.9	✓ Ro5	✓ Clean	`O=C(CCC(=O)c1ccccn1)c1ccccn1`
ZINC1070912 ZINC	0.611	286.3 Da LogP 4.15 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1)c1ccc(C(=O)c2ccccc2)cc1`
ZINC134079 ZINC	0.611	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789 ZINC	0.611	374.3 Da LogP 3.55 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)c3ccc(C(=O)O)cc3)cc…`
ZINC2146859 ZINC	0.611	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC3147211 ZINC	0.611	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC1613560 ZINC	0.607	216.2 Da LogP 2.21 TPSA 67.5	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1ccco1`
ZINC22418 ZINC	0.607	296.3 Da LogP 1.07 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(c1ccccn1)N1CCN(C(=O)c2ccccn2)CC1`
ZINC100477623 ZINC	0.600	204.2 Da LogP 2.33 TPSA 60.4	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccco1)c1ccco1`
ZINC2539781 ZINC	0.600	382.1 Da LogP 4.24 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(c1ccccc1)C(Br)(Br)C(=O)c1ccccc1`
ZINC6472822 ZINC	0.600	218.2 Da LogP 2.72 TPSA 60.4	✓ Ro5	✓ Clean	`O=C(CCC(=O)c1ccco1)c1ccco1`
ZINC82505816 ZINC	0.600	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccccn2)cn1`
ZINC83983988 ZINC	0.600	200.2 Da LogP 1.84 TPSA 63.1	✓ Ro5	✓ Clean	`O=C(O)c1cc(-c2ccccn2)ccn1`
ZINC156403 ZINC	0.593	274.3 Da LogP 1.47 TPSA 66.9	✓ Ro5	✓ Clean	`O=C(c1ccco1)N1CCN(C(=O)c2ccco2)CC1`
ZINC100009533 ZINC	0.591	226.2 Da LogP 3.80 TPSA 62.0	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N\c2ccccc2)cc1`
ZINC12956625 ZINC	0.591	226.2 Da LogP 3.80 TPSA 62.0	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccccc2)cc1`
ZINC1601737 ZINC	0.591	213.2 Da LogP 3.13 TPSA 49.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Nc2ccccc2)cc1`
ZINC1689689 ZINC	0.591	228.3 Da LogP 2.82 TPSA 61.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NNc2ccccc2)cc1`
ZINC1697492 ZINC	0.591	212.2 Da LogP 2.98 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Cc2ccccc2)cc1`
ZINC169818652 ZINC	0.591	380.5 Da LogP 2.76 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc([Si](c2ccccc2)(c2ccccc2)c2ccccc2)cc1`
ZINC33759110 ZINC	0.591	224.3 Da LogP 3.56 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/c2ccccc2)cc1`
ZINC346053 ZINC	0.591	289.3 Da LogP 4.85 TPSA 40.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(N(c2ccccc2)c2ccccc2)cc1`
ZINC396612 ZINC	0.591	230.3 Da LogP 3.54 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Sc2ccccc2)cc1`
ZINC409186 ZINC	0.591	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1cccc(C(=O)c2ccccc2)c1`
ZINC409394 ZINC	0.591	226.3 Da LogP 3.17 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(CCc2ccccc2)cc1`
ZINC4299335 ZINC	0.591	222.2 Da LogP 2.78 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C#Cc2ccccc2)cc1`
ZINC4403618 ZINC	0.591	226.2 Da LogP 3.80 TPSA 62.0	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccccc2)cc1`
ZINC4802802 ZINC	0.591	288.3 Da LogP 4.57 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(c2ccccc2)c2ccccc2)cc1`
ZINC5538754 ZINC	0.591	304.3 Da LogP 3.67 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(O)(c2ccccc2)c2ccccc2)cc1`
ZINC60939 ZINC	0.591	214.2 Da LogP 3.18 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccccc2)cc1`
ZINC4430796 ZINC	0.586	225.2 Da LogP 2.54 TPSA 47.0	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccccn1)c1ccccc1`
ZINC254583 ZINC	0.583	242.2 Da LogP 2.60 TPSA 63.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccccc2)cc1`
ZINC43214128 ZINC	0.583	240.3 Da LogP 2.81 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(CC(=O)c2ccccc2)cc1`
ZINC78349 ZINC	0.583	241.2 Da LogP 2.64 TPSA 66.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ccccc2)cc1`
ZINC19367002 ZINC	0.579	204.2 Da LogP -0.98 TPSA 81.1	✓ Ro5	✓ Clean	`CN(CCN(C)CC(=O)O)CC(=O)O`
ZINC4530702 ZINC	0.579	224.3 Da LogP 3.14 TPSA 34.1	✓ Ro5	✓ Clean	`O=C(CC(=O)c1ccccc1)c1ccccc1`
ZINC96315996 ZINC	0.579	268.3 Da LogP 2.77 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)/C(=C(\C(=O)O)c1ccccc1)c1ccccc1`

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.