Ligand profile

X52

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

Bound to: VK055_0016 — cytosine-specific methyltransferase

Via homolog PDB 6x9j UniProt P26358 Formula C₂₂H₂₈N₆O₂S₂
Mol. weight 472.64 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
X52
PDB
6x9j
UniProt (similar protein)
P26358
Target protein
VK055_0016

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 472.64 Da
LogP (Crippen) 2.73
H-bond donors 1
H-bond acceptors 8
TPSA 113.12 Ų
Rotatable bonds 10
Aromatic rings 2 / 2
Heavy atoms 32
Fraction sp³ C 0.41
Formula C₂₂H₂₈N₆O₂S₂

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 113.1
  • −1 ≤ LogP ≤ 5 2.73
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 472.6
  • LogP ≤ 5 2.73
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 113.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCc1c(c(nc(c1C#N)SCc2ccc(cc2)N(C)S(=O)(=O)C)N(C)CCNC)C#N
InChI 
InChI=1S/C22H28N6O2S2/c1-6-18-19(13-23)21(27(3)12-11-25-2)26-22(20(18)14-24)31-15-16-7-9-17(10-8-16)28(4)32(5,29)30/h7-10,25H,6,11-12,15H2,1-5H3
InChIKey 
GQHBHKILJGTNGL-UHFFFAOYSA-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
PF00145

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_0016.

PDB 2

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

Ligand PDB entry

ChEMBL 14

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)