Ligand profile

9CA

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

Bound to: VK055_4111 — rieske [2Fe-2S] domain protein

Via homolog PDB 2de7 UniProt Q84II6 Formula C₁₂H₉N
Mol. weight 167.21 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9CA
PDB
2de7
UniProt (similar protein)
Q84II6
Target protein
VK055_4111

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 167.21 Da
LogP (Crippen) 3.32
H-bond donors 1
H-bond acceptors 0
TPSA 15.79 Ų
Rotatable bonds 0
Aromatic rings 3 / 3
Heavy atoms 13
Fraction sp³ C 0.00
Formula C₁₂H₉N

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 15.8
  • −1 ≤ LogP ≤ 5 3.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 167.2
  • LogP ≤ 5 3.32
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 0
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 15.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)c3ccccc3[nH]2
InChI 
InChI=1S/C12H9N/c1-3-7-11-9(5-1)10-6-2-4-8-12(10)13-11/h1-8,13H
InChIKey 
UJOBWOGCFQCDNV-UHFFFAOYSA-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
PF11723

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_4111.

PDB 12

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)