Ligand profile

ZINC39204543

Virtual-screening candidate from ZINC.

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

Via homolog UniProt P40947 Formula C₂₁H₂₀O₁₃
Tanimoto 0.59
Mol. weight 480.38 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC39204543
UniProt (similar protein)
P40947
Tanimoto
0.588
Target protein
KP13_00396

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 480.38 Da
LogP (Crippen) -0.83
H-bond donors 9
H-bond acceptors 13
TPSA 230.74 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 34
Fraction sp³ C 0.29
Formula C₂₁H₂₀O₁₃

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 230.7
  • −1 ≤ LogP ≤ 5 -0.83
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 480.4
  • LogP ≤ 5 -0.83
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 230.7
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(-c2cc(O)c(O)c(O[C@@H]3O[C@H](CO)[C@@H](O)[C@H](O)[C@H]3O)c2)oc2cc(O)cc(O)c12
InChI 
InChI=1S/C21H20O13/c22-5-12-15(27)17(29)19(31)21(34-12)33-11-2-6(1-9(25)14(11)26)20-18(30)16(28)13-8(24)3-7(23)4-10(13)32-20/h1-4,12,15,17,19,21-27,29-31H,5H2/t12-,15-,17+,19-,21-/m1/s1
InChIKey 
ZJYAVUPWMNHHEU-GFOOFYSOSA-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)