Ligand profile

ZINC2560970

Virtual-screening candidate from ZINC.

Bound to: KP13_02757 — Cystathionine beta-lyase

Via homolog UniProt Q8VCN5 Formula C₉H₁₂N₂O₅
Tanimoto 0.50
Mol. weight 228.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2560970
UniProt (similar protein)
Q8VCN5
Tanimoto
0.500
Target protein
KP13_02757

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 228.20 Da
LogP (Crippen) -1.62
H-bond donors 4
H-bond acceptors 4
TPSA 129.72 Ų
Rotatable bonds 6
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.44
Formula C₉H₁₂N₂O₅

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy Check

Estimated from TPSA and LogP only: TPSA ≤ 90 Ų and −1 ≤ LogP ≤ 5 are treated as a favorable small-molecule permeability screen.

  • TPSA ≤ 90 Ų 129.7
  • −1 ≤ LogP ≤ 5 -1.62
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 228.2
  • LogP ≤ 5 -1.62
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 129.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C#CC[C@H](NC(=O)[C@@H](N)CC(=O)O)C(=O)O
InChI 
InChI=1S/C9H12N2O5/c1-2-3-6(9(15)16)11-8(14)5(10)4-7(12)13/h1,5-6H,3-4,10H2,(H,11,14)(H,12,13)(H,15,16)/t5-,6-/m0/s1
InChIKey 
WIHFMPVINVRCJZ-WDSKDSINSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
CHEMBL4795578
Homolog
Q8VCN5

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02757.

PDB 6

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 2

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 23

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)