Ligand profile

ZINC59765976

Virtual-screening candidate from ZINC.

Bound to: KP13_00396 — Single-stranded DNA-binding protein

Via homolog UniProt P40947 Formula C₂₀H₁₈O₁₂
Tanimoto 0.56
Mol. weight 450.35 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC59765976
UniProt (similar protein)
P40947
Tanimoto
0.560
Target protein
KP13_00396

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 450.35 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 32
Fraction sp³ C 0.25
Formula C₂₀H₁₈O₁₂

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 450.4
  • 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 
O=c1c(O[C@@H]2OC[C@H](O)[C@H](O)[C@H]2O)c(-c2cc(O)c(O)c(O)c2)oc2cc(O)cc(O)c12
InChI 
InChI=1S/C20H18O12/c21-7-3-8(22)13-12(4-7)31-18(6-1-9(23)14(26)10(24)2-6)19(16(13)28)32-20-17(29)15(27)11(25)5-30-20/h1-4,11,15,17,20-27,29H,5H2/t11-,15-,17+,20-/m0/s1
InChIKey 
SBEOEJNITMVWLK-KJCLSZHRSA-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 KP13_00396.

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)