Ligand profile

ZINC2873978

Virtual-screening candidate from ZINC.

Bound to: KP13_02076 — Nuclease sbcCD subunit D

Via homolog UniProt Q9X1X0 Formula C₂₀H₁₉NO₄S₂
Tanimoto 0.82
Mol. weight 401.51 Da
Permeability High
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2873978
UniProt (similar protein)
Q9X1X0
Tanimoto
0.822
Target protein
KP13_02076

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 401.51 Da
LogP (Crippen) 4.03
H-bond donors 1
H-bond acceptors 6
TPSA 56.79 Ų
Rotatable bonds 8
Aromatic rings 2 / 3
Heavy atoms 27
Fraction sp³ C 0.20
Formula C₂₀H₁₉NO₄S₂

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 56.8
  • −1 ≤ LogP ≤ 5 4.03
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 401.5
  • LogP ≤ 5 4.03
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 56.8
PAINS Alert

Matches PAINS filter: ene_rhod_A(235). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cccc(OCCCOc2cccc(/C=C3/SC(=S)NC3=O)c2)c1
InChI 
InChI=1S/C20H19NO4S2/c1-23-15-6-3-8-17(13-15)25-10-4-9-24-16-7-2-5-14(11-16)12-18-19(22)21-20(26)27-18/h2-3,5-8,11-13H,4,9-10H2,1H3,(H,21,22,26)/b18-12+
InChIKey 
OCBKIQADKKSROR-LDADJPATSA-N

Provenance

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

Method
LigQ nearest_k
Query
UKV
Homolog
Q9X1X0

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_02076.

PDB 7

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)