Ligand profile

CHEMBL399890

Bioactivity hit from ChEMBL on a similar protein.

Bound to: VK055_5159 — DNA adenine methylase family protein

Via homolog UniProt P0AEE8 Formula C₁₃H₁₇N₅O₅S
Mol. weight 355.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CHEMBL399890
UniProt (similar protein)
P0AEE8
Target protein
VK055_5159

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 355.38 Da
LogP (Crippen) -0.76
H-bond donors 4
H-bond acceptors 10
TPSA 156.61 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 24
Fraction sp³ C 0.54
Formula C₁₃H₁₇N₅O₅S

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 156.6
  • −1 ≤ LogP ≤ 5 -0.76
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 355.4
  • LogP ≤ 5 -0.76
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 156.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCCC(=O)O)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C13H17N5O5S/c14-11-8-12(16-4-15-11)18(5-17-8)13-10(22)9(21)6(23-13)3-24-2-1-7(19)20/h4-6,9-10,13,21-22H,1-3H2,(H,19,20)(H2,14,15,16)/t6-,9-,10-,13-/m1/s1
InChIKey 
JXYJDRSYWXIEQE-ZRFIDHNTSA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Activity
Active
Binding sites
PF02086

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_5159.

ChEMBL 2

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)