KpKP13 Protein target profile

Cystathionine beta-lyase

Accession: KP13_02757

Gene: metC AHE42674.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GTB9

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Length 362

Pocket druggability (P2Rank · AlphaFold DB model) 0.712

Direct ligand evidence 0 32 total records

Functional annotation 0 EC 8 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 0.52. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.71. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 6 structural and 2 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 (%): 48.619 Lower values reduce human off-target concern.
Human E-value: 3.98e-111
Gut microbiome similarity: 3.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 42.978 Higher values support similarity to known essential genes.
DEG E-value: 2.23e-102 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 96.95 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) 0.712

Structure A0A0H3GTB9

Pocket Pocket 1

Druggability (FPocket) 0.519

Structure A0A0H3GTB9

Pocket Pocket 1

ColabFold model

P2Rank 0.675 · Pocket 1

FPocket 0.55 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 182 / 4744 genomes with a hit

Prevalence 3.8%

Sequence

Primary amino-acid sequence viewer.

MMPPIYATSTFAQPAPGQHTGYEYSRSGNPTRHALETAIADLENGTRGYAFASGLAAISTVLELLDKDSHLVAVDDVYGGTYRLLENVRRRSAGLQVSWVKPDDLAGIEAAIRPDTRMIWVETPTNPLLKLADLSAIAAIARRHNLISVADNTFASPAIHRPLEHGFDIVVHSATKYLNGHSDVVAGLAVVGDNSGLAEKLGYLQNAVGGVLDPFSSFLTLRGIRTLALRMERHSANALQLAEWLEQQPEVERVWFPWLASHPHHQLARQQMALPGGMISVVVKGDEGYAERIISKLRWFTLAESLGGVESLVSQPFSMTHASIPLEKRLANGITPQLIRLSVGIEDPNDLIADWQQALRAE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0019346 The interconversion of homocysteine and cysteine via cystathionine. In contrast with enteric bacteria and mammals, Saccharomyces cerevisiae has two transsulfuration pathways employing two separate sets of enzymes.
GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0004123 Catalysis of the reaction: L-cystathionine + H2O = 2-oxobutanoate + L-cysteine + NH4+.
GO:0003962 Catalysis of the reaction: L-cysteine + O-succinyl-L-homoserine = H+ + L,L-cystathionine + succinate.
GO:0019343 OBSOLETE. The chemical reactions and pathways resulting in the formation of L-cysteine, via the intermediate L-cystathionine.
GO:0009086 OBSOLETE. The chemical reactions and pathways resulting in the de novo formation of L-methionine (2-amino-4-(methylthio)butanoic acid), a sulfur-containing, essential amino acid found in peptide linkage in proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
168	182	ProSitePatterns	PS00868	Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.
168	182	InterPro	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
1	226	Gene3D	G3DSA:3.40.640.10	-
1	226	InterPro	IPR015421	Pyridoxal phosphate-dependent transferase, major domain
228	362	FunFam	G3DSA:3.90.1150.10:FF:000033	Cystathionine gamma-synthase
227	361	Gene3D	G3DSA:3.90.1150.10	Aspartate Aminotransferase, domain 1
227	361	InterPro	IPR015422	Pyridoxal phosphate-dependent transferase, small domain
1	226	FunFam	G3DSA:3.40.640.10:FF:000009	Cystathionine gamma-synthase homolog
3	360	CDD	cd00614	CGS_like
3	360	InterPro	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
2	359	Pfam	PF01053	Cys/Met metabolism PLP-dependent enzyme
2	359	InterPro	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
1	362	PIRSF	PIRSF001434	CGS
1	362	InterPro	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
2	361	PANTHER	PTHR11808	TRANS-SULFURATION ENZYME FAMILY MEMBER
2	361	InterPro	IPR000277	Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
4	360	SUPERFAMILY	SSF53383	PLP-dependent transferases
4	360	InterPro	IPR015424	Pyridoxal phosphate-dependent transferase

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

0.712

Likely same site as FPocket 1 1.0 Å 17 shared residues 100% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.194

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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

0.519

Likely same site as P2Rank 1 1.0 Å 17 shared residues 100% of smaller site

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_A0A0H3GTB9	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02757	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.

32 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records

Transferred evidence 8 records from similar proteins

Structural ligands 6 0 loaded crystals

Measured bioactivity 2 direct and transferred ChEMBL records

Proposed compounds 24 similarity-based ZINC candidates

Best available ligand signal

0JO PDB via homolog 316.2 Da · LogP 0.72 · TPSA 149.5 Open detail RCSB PDB

E9U PDB via homolog Detail RCSB PDB

F0G PDB via homolog Detail RCSB PDB

KOU PDB via homolog Detail RCSB PDB

NAK 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
0JO RCSB PDB	4IYO	Q5H4T8	316.2 Da LogP 0.72 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/C(=C)C(=O)O)O`
E9U RCSB PDB	6LE4	F9UT53	451.4 Da LogP 0.11 TPSA 212.9	1 viol.	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H](CCSC[C@@H]…`
F0G RCSB PDB	6CJA	Q5ZX43	318.2 Da LogP 0.60 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H](C)C(=O)O)O`
KOU RCSB PDB	6LDO	F9UT53	334.2 Da LogP -0.43 TPSA 169.8	✓ Ro5	✓ Clean	`Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/C(CO)C(=O)O)O`
NAK RCSB PDB	4IYO	Q5H4T8	87.1 Da LogP -3.04 TPSA 65.7	✓ Ro5	✓ Clean	`CC(=[NH2+])C(=O)[O-]`
PYR RCSB PDB	6K1L	B4SII9	88.1 Da LogP -0.34 TPSA 54.4	✓ Ro5	✓ Clean	`CC(=O)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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL4795578 ChEMBL	Q8VCN5	—	113.1 Da LogP -0.58 TPSA 63.3	✓ Ro5	✓ Clean	`C#CCC(N)C(=O)O`
QU4 ChEMBL	Q8VCN5	—	422.3 Da LogP 2.45 TPSA 169.4	✓ Ro5	✓ Clean	`c1cc(c(cc1C(=C2C=CC(=O)C(=C2)C(=O)O)c3ccc(c(c3)…`

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
ZINC3833863 ZINC	1.000	422.3 Da LogP 2.45 TPSA 169.4	✓ Ro5	✓ Clean	`O=C(O)C1=CC(=C(c2ccc(O)c(C(=O)O)c2)c2ccc(O)c(C(…`
ZINC2054344316 ZINC	0.756	300.3 Da LogP 2.01 TPSA 111.9	✓ Ro5	✓ Clean	`CC(=C1C=CC(=O)C(C(=O)O)=C1)c1ccc(O)c(C(=O)O)c1`
ZINC28092924 ZINC	0.756	300.3 Da LogP 2.01 TPSA 111.9	✓ Ro5	✓ Clean	`C/C(=C1/C=CC(=O)C(C(=O)O)=C1)c1ccc(O)c(C(=O)O)c1`
ZINC36748824 ZINC	0.756	300.3 Da LogP 2.01 TPSA 111.9	✓ Ro5	✓ Clean	`C/C(=C1\C=CC(=O)C(C(=O)O)=C1)c1ccc(O)c(C(=O)O)c1`
ZINC1532514 ZINC	0.646	247.1 Da LogP 0.52 TPSA 117.0	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C=O)c1O`
ZINC64708385 ZINC	0.644	467.4 Da LogP 0.44 TPSA 214.5	1 viol.	✓ Clean	`NOC(=O)C1=CC(=C(c2ccc(O)c(C(=O)ON)c2)c2ccc(O)c(…`
ZINC2114966 ZINC	0.643	332.2 Da LogP 0.99 TPSA 149.5	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/CCCC(=O)O)c1O`
ZINC6824902 ZINC	0.576	401.2 Da LogP 3.22 TPSA 112.2	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/c2ccccc2Br)c1O`
ZINC2527979 ZINC	0.564	296.3 Da LogP 0.32 TPSA 140.3	✓ Ro5	✓ Clean	`Cc1ncc(CO)c(/C=N/[C@@H](CCC(=O)O)C(=O)O)c1O`
ZINC1656021 ZINC	0.551	233.2 Da LogP 1.01 TPSA 99.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(C)c1O`
ZINC1532705 ZINC	0.549	249.2 Da LogP 0.20 TPSA 120.1	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CO)c1O`
ZINC111474396 ZINC	0.544	280.3 Da LogP 1.51 TPSA 103.0	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](/N=C\c1c(CO)cnc(C)c1O)C(=O)O`
ZINC2527980 ZINC	0.544	280.3 Da LogP 1.51 TPSA 103.0	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](/N=C/c1c(CO)cnc(C)c1O)C(=O)O`
ZINC1532708 ZINC	0.538	248.2 Da LogP 0.16 TPSA 125.9	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(CN)c1O`
ZINC9944295 ZINC	0.522	400.4 Da LogP 1.30 TPSA 149.4	✓ Ro5	✓ Clean	`Cc1ncc(COP(=O)(O)O)c(/C=N/NC(=S)NCc2ccco2)c1O`
ZINC12671061 ZINC	0.520	346.4 Da LogP 4.29 TPSA 74.6	✓ Ro5	✓ Clean	`CC1=C/C(=C(/c2ccc(O)c(C)c2)c2ccccc2C(=O)O)C=CC1…`
ZINC3953836 ZINC	0.520	346.4 Da LogP 4.29 TPSA 74.6	✓ Ro5	✓ Clean	`CC1=C/C(=C(\c2ccc(O)c(C)c2)c2ccccc2C(=O)O)C=CC1…`
ZINC12503280 ZINC	0.510	302.2 Da LogP 1.01 TPSA 136.3	✓ Ro5	Alert	`O=C(O)C1=C/C(=N\Nc2ccc(O)c(C(=O)O)c2)C=CC1=O`
ZINC95536736 ZINC	0.510	302.2 Da LogP 1.01 TPSA 136.3	✓ Ro5	Alert	`O=C(O)C1=C/C(=N/Nc2ccc(O)c(C(=O)O)c2)C=CC1=O`
ZINC127634755 ZINC	0.500	228.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C#CC[C@H](NC(=O)[C@H](N)CC(=O)O)C(=O)O`
ZINC127634920 ZINC	0.500	228.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C#CC[C@@H](NC(=O)[C@H](N)CC(=O)O)C(=O)O`
ZINC127635164 ZINC	0.500	228.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C#CC[C@@H](NC(=O)[C@@H](N)CC(=O)O)C(=O)O`
ZINC1701223 ZINC	0.500	302.2 Da LogP 1.73 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(c1ccc(O)c(C(=O)O)c1)c1ccc(O)c(C(=O)O)c1`
ZINC2560970 ZINC	0.500	228.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`C#CC[C@H](NC(=O)[C@@H](N)CC(=O)O)C(=O)O`

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 A0A0H3GTB9

Chemistry

ChEMBL CHEMBL4795578 ChEMBL QU4