Ligand profile

PDN

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_02277 — Protein tas

Via homolog PDB 3eb3 UniProt P62483 Formula C₂₁H₂₆O₅
Mol. weight 358.43 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PDN
PDB
3eb3
UniProt (similar protein)
P62483
Target protein
KP13_02277

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 358.43 Da
LogP (Crippen) 3.16
H-bond donors 3
H-bond acceptors 5
TPSA 94.83 Ų
Rotatable bonds 1
Aromatic rings 0 / 4
Heavy atoms 26
Fraction sp³ C 0.62
Formula C₂₁H₂₆O₅

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 94.8
  • −1 ≤ LogP ≤ 5 3.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 358.4
  • LogP ≤ 5 3.16
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 94.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@]12CC(=O)[C@H]3[C@H]([C@@H]1CC[C@@]2(C(=CO)O)O)CCC4=CC(=O)C=C[C@]34C
InChI 
InChI=1S/C21H26O5/c1-19-7-5-13(23)9-12(19)3-4-14-15-6-8-21(26,17(25)11-22)20(15,2)10-16(24)18(14)19/h5,7,9,11,14-15,18,22,25-26H,3-4,6,8,10H2,1-2H3/t14-,15-,18+,19-,20-,21-/m0/s1
InChIKey 
WZTZVUUYKIOIRV-ZPOLXVRWSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00248

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_02277.

PDB 5

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)