Ligand profile

ZINC19368612

Virtual-screening candidate from ZINC.

Bound to: KP13_05461 — Periplasmic murein peptide-binding protein

Via homolog UniProt P33590 Formula C₂₀H₂₄N₂O₆
Tanimoto 1.00
Mol. weight 388.42 Da
Permeability Check
PAINS Alert

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC19368612
UniProt (similar protein)
P33590
Tanimoto
1.000
Target protein
KP13_05461

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 388.42 Da
LogP (Crippen) 1.57
H-bond donors 4
H-bond acceptors 6
TPSA 121.54 Ų
Rotatable bonds 11
Aromatic rings 2 / 2
Heavy atoms 28
Fraction sp³ C 0.30
Formula C₂₀H₂₄N₂O₆

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 121.5
  • −1 ≤ LogP ≤ 5 1.57
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 388.4
  • LogP ≤ 5 1.57
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 121.5
PAINS Alert

Matches PAINS filter: mannich_A(296). May be a frequent false positive in HTS — review carefully.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)CN(CCN(CC(=O)O)Cc1ccccc1O)Cc1ccccc1O
InChI 
InChI=1S/C20H24N2O6/c23-17-7-3-1-5-15(17)11-21(13-19(25)26)9-10-22(14-20(27)28)12-16-6-2-4-8-18(16)24/h1-8,23-24H,9-14H2,(H,25,26)(H,27,28)
InChIKey 
GRUVVLWKPGIYEG-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
BHN
Homolog
P33590

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_05461.

PDB 21

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)