Protein profile

VK055_4046

cystathionine beta-lyase

Genome: KpATCC43816

Gene: AIK82593.1 metC2 Structure source: Experimental + ColabFold UniProt A0A0H3GVN6
Amino acids 395
Annotations 10
Features 20
PDB binders 17
Druggability 0.673

Overview

Basic information about this protein and its source genome.

Accession
VK055_4046
Gene
AIK82593.1 metC2
Status
annotated
Amino acids
395
Structure source
Experimental + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
31.902
Human E-value
4.89e-47
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
65.296
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
97.16

Selected Druggability evidence

PDB experimental structure

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.673
Structure 8DUY
Pocket Pocket 2
P2Rank 0.637
Structure 8DUY
Pocket Pocket 1
ColabFold model
FPocket 0.333 · Pocket 14
P2Rank 0.549 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 132 / 4744 genomes with a hit
Normalized 0.028

Sequence

Primary amino-acid sequence viewer.

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: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: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:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • 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 Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
7 391 Pfam PF01053 Cys/Met metabolism PLP-dependent enzyme
7 391 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
202 216 ProSitePatterns PS00868 Cys/Met metabolism enzymes pyridoxal-phosphate attachment site.
202 216 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
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
259 395 FunFam G3DSA:3.90.1150.10:FF:000058 Cystathionine beta-lyase
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
259 395 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
259 395 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
1 395 PIRSF PIRSF001434 CGS
1 395 InterPro IPR000277 Cys/Met metabolism, pyridoxal phosphate-dependent enzyme
1 258 FunFam G3DSA:3.40.640.10:FF:000062 Cystathionine beta-lyase

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different 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 VK055_4046
ColabFold full sequence Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
3 0.942
4 0.853
2 0.588
5 0.264

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 31.37 0.939
2 30.07 0.933
3 29.81 0.933
4 27.13 0.919
5 27.06 0.918

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

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 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 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 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 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 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 Q84AR1 149.2 Da LogP 0.15 TPSA 63.3 ✓ Ro5 ✓ Clean CCSC[C@@H](C(=O)O)N
IN5 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 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 Q86D28 48.1 Da LogP 0.55 TPSA 0.0 ✓ Ro5 ✓ Clean CS
MPJ Q84AR1 169.2 Da LogP 0.49 TPSA 63.3 ✓ Ro5 ✓ Clean CSCC[C@H](N)[P@H](=O)O
NLE A0A0A5P8W7 131.2 Da LogP 0.59 TPSA 63.3 ✓ Ro5 ✓ Clean CCCC[C@@H](C(=O)O)N
P3F 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 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 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 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 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 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.