Ligand profile

ZINC13130924

Virtual-screening candidate from ZINC.

Bound to: VK055_3025 — ssDNA-binding protein

Via homolog UniProt P40947 Formula C₂₀H₁₈O₆
Tanimoto 0.55
Mol. weight 354.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13130924
UniProt (similar protein)
P40947
Tanimoto
0.551
Target protein
VK055_3025

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 354.36 Da
LogP (Crippen) 3.79
H-bond donors 4
H-bond acceptors 6
TPSA 111.13 Ų
Rotatable bonds 3
Aromatic rings 3 / 3
Heavy atoms 26
Fraction sp³ C 0.15
Formula C₂₀H₁₈O₆

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 111.1
  • −1 ≤ LogP ≤ 5 3.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 354.4
  • LogP ≤ 5 3.79
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 111.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)=CCc1cc(-c2oc3cc(O)cc(O)c3c(=O)c2O)ccc1O
InChI 
InChI=1S/C20H18O6/c1-10(2)3-4-11-7-12(5-6-14(11)22)20-19(25)18(24)17-15(23)8-13(21)9-16(17)26-20/h3,5-9,21-23,25H,4H2,1-2H3
InChIKey 
PGCKDCPTJAQQSQ-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
MYC
Homolog
P40947

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_3025.

PDB 2

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)