Protein target profile

KP13_02775

Cystathionine beta-lyase metC

Genome: KpKP13 Gene: AHE42656.1 3D evidence: Experimental + ColabFold model UniProt A0A0H3GVN6
Length 395
Pocket druggability 0.673
Direct ligand evidence 0 71 total records
Functional annotation 1 EC 9 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 (%)
31.902 Lower values reduce human off-target concern.
Human E-value
4.89e-47
Gut microbiome similarity
2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
65.296 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.13 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.673
Structure 8DUY
Pocket Pocket 2
P2Rank 0.637
Structure 8DUY
Pocket Pocket 1
ColabFold model
FPocket 0.197 · Pocket 16
P2Rank 0.526 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 132 / 4744 genomes with a hit
Prevalence 2.8%

Cross-references

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

Structure

Sequence

Primary amino-acid sequence viewer.

MADKHLDTALVNAGRSKKYTQGSVNSVIQRASSLVFDTVEAKKHATRNRANGELFYGRRGTLTHFSLQEAMCELEGGAGCALFPCGAAAVANTILAFVEQGDHVLMTNTAYEPSQDFCTKILAKLGVTTSWFDPLIGADIARLVRPETRVVFLESPGSITMEVHDVPAIVAAVRQVAPEAIIMIDNTWAAGILFKALDFGIDISIQAGTKYLIGHSDAMVGTAVANARCWPQLRENAYLMGQMLDADTAYMTSRGLRTLGVRLRQHHESSLRIAEWLAQHPQVARVNHPALPGSKGHEFWKRDFTGSSGLFSFVLSKRLNDAELAEYLDNFSLFSMAYSWGGFESLILANQPEQIAHIRPDAEVDFSGTLIRLHIGLENVDDLQADLAAGFARIV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0004121 OBSOLETE. Catalysis of the reaction: cystathionine + H2O = L-homocysteine + NH3 + pyruvate.
  • GO:0006520 The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups.
  • 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: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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0047804 Catalysis of the reaction: S-substituted L-cysteine + H2O = a thiol + NH4+ + pyruvate.
  • GO:0019450 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-cysteine into other compounds, including pyruvate.
  • 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.

20 records
Show feature table
Start End DB Term Name
1 258 Gene3D G3DSA:3.40.640.10 -
1 258 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
8 394 NCBIfam TIGR01324 cystathionine beta-lyase
8 394 InterPro IPR006233 Cystathionine beta-lyase, bacterial
202 216 ProSitePatterns PS00868 Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.
202 216 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
259 395 FunFam G3DSA:3.90.1150.10:FF:000058 Cystathionine beta-lyase
1 258 FunFam G3DSA:3.40.640.10:FF:000062 Cystathionine beta-lyase
24 393 SUPERFAMILY SSF53383 PLP-dependent transferases
24 393 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
22 392 CDD cd00614 CGS_like
22 392 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
1 395 PIRSF PIRSF001434 CGS
1 395 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
3 394 PANTHER PTHR43500 CYSTATHIONINE BETA-LYASE-RELATED
3 394 InterPro IPR006233 Cystathionine beta-lyase, bacterial
7 391 Pfam PF01053 Cys/Met metabolism PLP-dependent enzyme
7 391 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
259 395 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
259 395 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain

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
0.673
Likely same site as P2Rank 1 3.5 Å 14 shared residues 93% 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
0.637
Likely same site as FPocket 2 3.5 Å 14 shared residues 93% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.427
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Surrounding area
Site 3 P2Rank #3
0.112
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.015
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Surrounding area
Site 5 P2Rank #5
0.015
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Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 8DUY
X-ray 1.90 Å A,B,C,D
100.0% 1-395
Viewing
ColabFold KP13_02775
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.

71 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 21 records from similar proteins
Structural ligands 17 0 loaded crystals
Measured bioactivity 4 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2LM PDB via homolog 378.3 Da · LogP 1.48 · TPSA 149.5 Open detail RCSB PDB
3LM PDB via homolog Detail RCSB PDB
4LM PDB via homolog Detail RCSB PDB
AA5 PDB via homolog Detail RCSB PDB
BLP 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
2LM RCSB PDB Q86D28 378.3 Da LogP 1.48 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C(\CCSC)/C(=O)O)O
3LM RCSB PDB Q86D28 378.3 Da LogP 1.13 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN/C(=C/CSC)/C(=O)O)O
4LM RCSB PDB Q86D28 330.2 Da LogP 1.11 TPSA 149.5 ✓ Ro5 ✓ Clean C/C=C(\C(=O)O)/N=C/c1c(cnc(c1O)C)COP(=O)(O)O
AA5 RCSB PDB Q86D28 378.3 Da LogP 1.33 TPSA 149.5 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C=N[C@@H](CCSC)C(=O)O)O
BLP RCSB PDB P06721 469.3 Da LogP 0.16 TPSA 213.2 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNNC(=O)CNC(=O)c2ccccc…
ECX RCSB PDB Q84AR1 149.2 Da LogP 0.15 TPSA 63.3 ✓ Ro5 ✓ Clean CCSC[C@@H](C(=O)O)N
IN5 RCSB PDB P06721 356.2 Da LogP 0.32 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](C)P(=O)(O)O)O
LCS RCSB PDB Q84AR1 331.2 Da LogP -0.29 TPSA 150.6 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C/2\CONC2=O)O
MEE RCSB PDB Q86D28 48.1 Da LogP 0.55 TPSA 0.0 ✓ Ro5 ✓ Clean CS
MPJ RCSB PDB Q84AR1 169.2 Da LogP 0.49 TPSA 63.3 ✓ Ro5 ✓ Clean CSCC[C@H](N)[P@H](=O)O
NLE RCSB PDB A0A0A5P8W7 131.2 Da LogP 0.59 TPSA 63.3 ✓ Ro5 ✓ Clean CCCC[C@@H](C(=O)O)N
P3F RCSB PDB P06721 490.3 Da LogP 1.60 TPSA 170.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\NC(=O)CNC(=O)c2cc…
PLG RCSB PDB Q84AR1 306.2 Da LogP -0.12 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
PPG RCSB PDB P06721 389.3 Da LogP 0.22 TPSA 184.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C/N=C(\C=C\OCCN)/C(=O)…
PPJ RCSB PDB A2FEV4 362.3 Da LogP 0.35 TPSA 169.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)\C=N\[C@@H](C[C@H](C)O…
PY6 RCSB PDB A0A0A5P8W7 362.3 Da LogP 1.44 TPSA 149.2 ✓ Ro5 ✓ Clean CCCC[C@@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O)O
PZP RCSB PDB Q84AR1 246.2 Da LogP 0.70 TPSA 123.7 ✓ Ro5 ✓ Clean [H]/N=C/c1c(cnc(c1O)C)COP(=O)(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.