Ligand profile

R9T

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

Bound to: VK055_0478 — cfa

Via homolog PDB 5kok UniProt C3SBW0 Formula C₂₀H₂₅NO₄
Mol. weight 343.42 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
R9T
PDB
5kok
UniProt (similar protein)
C3SBW0
Target protein
VK055_0478

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 343.42 Da
LogP (Crippen) 3.15
H-bond donors 1
H-bond acceptors 5
TPSA 48.95 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 25
Fraction sp³ C 0.40
Formula C₂₀H₂₅NO₄

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 49.0
  • −1 ≤ LogP ≤ 5 3.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 343.4
  • LogP ≤ 5 3.15
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 49.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc(cc1OC)C[C@@H]2c3cc(c(cc3CCN2)OC)OC
InChI 
InChI=1S/C20H25NO4/c1-22-17-6-5-13(10-18(17)23-2)9-16-15-12-20(25-4)19(24-3)11-14(15)7-8-21-16/h5-6,10-12,16,21H,7-9H2,1-4H3/t16-/m1/s1
InChIKey 
YXWQTVWJNHKSCC-MRXNPFEDSA-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
PF02353

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_0478.

PDB 6

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)