Ligand profile

A3B

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

Bound to: VK055_0027 — D-cysteine desulfhydrase monomer

Via homolog PDB 1tzj UniProt Q00740 Formula C₄H₇NO₂
Mol. weight 101.10 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
A3B
PDB
1tzj
UniProt (similar protein)
Q00740
Target protein
VK055_0027

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 101.10 Da
LogP (Crippen) -2.47
H-bond donors 1
H-bond acceptors 2
TPSA 67.77 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 7
Fraction sp³ C 0.25
Formula C₄H₇NO₂

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 67.8
  • −1 ≤ LogP ≤ 5 -2.47
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 101.1
  • LogP ≤ 5 -2.47
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 67.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C=C[C@H](C(=O)[O-])[NH3+]
InChI 
InChI=1S/C4H7NO2/c1-2-3(5)4(6)7/h2-3H,1,5H2,(H,6,7)/t3-/m1/s1
InChIKey 
RQVLGLPAZTUBKX-GSVOUGTGSA-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
PF00291

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_0027.

PDB 9

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

Ligand PDB entry

ZINC 24

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

Compound Similarity (Tanimoto)