Ligand profile

NLE

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: VK055_4046 — cystathionine beta-lyase

Via homolog PDB 5m3z UniProt A0A0A5P8W7 Formula C₆H₁₃NO₂
Mol. weight 131.17 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NLE
PDB
5m3z
UniProt (similar protein)
A0A0A5P8W7
Target protein
VK055_4046

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 131.17 Da
LogP (Crippen) 0.59
H-bond donors 2
H-bond acceptors 2
TPSA 63.32 Ų
Rotatable bonds 4
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 0.83
Formula C₆H₁₃NO₂

Drug-likeness

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

Permeability proxy High

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 63.3
  • −1 ≤ LogP ≤ 5 0.59
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 131.2
  • LogP ≤ 5 0.59
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 63.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCC[C@@H](C(=O)O)N
InChI 
InChI=1S/C6H13NO2/c1-2-3-4-5(7)6(8)9/h5H,2-4,7H2,1H3,(H,8,9)/t5-/m0/s1
InChIKey 
LRQKBLKVPFOOQJ-YFKPBYRVSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01053

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4046.

PDB 16

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

Ligand PDB entry

ChEMBL 4

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

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)