Ligand profile

DF9

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

Bound to: VK055_2391 — MTA/SAH nucleosidase

Via homolog PDB 3df9 UniProt P0AF14 Formula C₁₉H₂₃N₅OS
Mol. weight 369.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DF9
PDB
3df9
UniProt (similar protein)
P0AF14
Target protein
VK055_2391

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 369.49 Da
LogP (Crippen) 2.27
H-bond donors 3
H-bond acceptors 6
TPSA 91.06 Ų
Rotatable bonds 6
Aromatic rings 3 / 4
Heavy atoms 26
Fraction sp³ C 0.37
Formula C₁₉H₂₃N₅OS

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 91.1
  • −1 ≤ LogP ≤ 5 2.27
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 369.5
  • LogP ≤ 5 2.27
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 91.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)CSC[C@H]2CN(C[C@@H]2O)Cc3c[nH]c4c3ncnc4N
InChI 
InChI=1S/C19H23N5OS/c20-19-18-17(22-12-23-19)14(6-21-18)7-24-8-15(16(25)9-24)11-26-10-13-4-2-1-3-5-13/h1-6,12,15-16,21,25H,7-11H2,(H2,20,22,23)/t15-,16+/m1/s1
InChIKey 
DIGGNILBPCEZIV-CVEARBPZSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF01048

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_2391.

PDB 10

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

Ligand PDB entry

ChEMBL 34

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)