Ligand profile

4F0

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

Bound to: VK055_2391 — MTA/SAH nucleosidase

Via homolog PDB 4yml UniProt P0AF12 Formula C₁₃H₁₉N₅OS
Mol. weight 293.40 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4F0
PDB
4yml
UniProt (similar protein)
P0AF12
Target protein
VK055_2391

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 293.40 Da
LogP (Crippen) 0.70
H-bond donors 3
H-bond acceptors 6
TPSA 91.06 Ų
Rotatable bonds 4
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.54
Formula C₁₃H₁₉N₅OS

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 0.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 293.4
  • LogP ≤ 5 0.70
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 91.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CSC[C@@H]1CN(C[C@H]1O)Cc2c[nH]c3c2ncnc3N
InChI 
InChI=1S/C13H19N5OS/c1-20-6-9-4-18(5-10(9)19)3-8-2-15-12-11(8)16-7-17-13(12)14/h2,7,9-10,15,19H,3-6H2,1H3,(H2,14,16,17)/t9-,10+/m0/s1
InChIKey 
NTHMDFGHOCNNOE-VHSXEESVSA-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)