Ligand profile

ZINC35092275

Virtual-screening candidate from ZINC.

Bound to: VK055_3025 — ssDNA-binding protein

Via homolog UniProt P40947 Formula C₂₁H₂₀O₁₂
Tanimoto 0.58
Mol. weight 464.38 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC35092275
UniProt (similar protein)
P40947
Tanimoto
0.580
Target protein
VK055_3025

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 464.38 Da
LogP (Crippen) 0.19
H-bond donors 8
H-bond acceptors 12
TPSA 210.51 Ų
Rotatable bonds 3
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.29
Formula C₂₁H₂₀O₁₂

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 210.5
  • −1 ≤ LogP ≤ 5 0.19
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 464.4
  • LogP ≤ 5 0.19
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 210.5
PAINS Alert

Matches PAINS filter: catechol_A(92). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1O[C@H](Oc2c(-c3cc(O)c(O)c(O)c3)oc3cc(O)cc(O)c3c2=O)[C@H](O)[C@H](O)[C@H]1O
InChI 
InChI=1S/C21H20O12/c1-6-14(26)17(29)18(30)21(31-6)33-20-16(28)13-9(23)4-8(22)5-12(13)32-19(20)7-2-10(24)15(27)11(25)3-7/h2-6,14,17-18,21-27,29-30H,1H3/t6-,14-,17+,18+,21+/m0/s1
InChIKey 
DCYOADKBABEMIQ-YIFFCZEQSA-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)