Ligand profile

PAM

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

Bound to: VK055_3233 — bacterial regulatory helix-turn-helix, AraC family protein

Via homolog PDB 3gbg UniProt A5F384 Formula C₁₆H₃₀O₂
Mol. weight 254.41 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PAM
PDB
3gbg
UniProt (similar protein)
A5F384
Target protein
VK055_3233

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 254.41 Da
LogP (Crippen) 5.33
H-bond donors 1
H-bond acceptors 1
TPSA 37.30 Ų
Rotatable bonds 13
Aromatic rings 0 / 0
Heavy atoms 18
Fraction sp³ C 0.81
Formula C₁₆H₃₀O₂

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 37.3
  • −1 ≤ LogP ≤ 5 5.33
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 254.4
  • LogP ≤ 5 5.33
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Fail
  • Rotatable bonds ≤ 10 13
  • TPSA ≤ 140 Ų 37.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCC\C=C/CCCCCCCC(=O)O
InChI 
InChI=1S/C16H30O2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16(17)18/h7-8H,2-6,9-15H2,1H3,(H,17,18)/b8-7-
InChIKey 
SECPZKHBENQXJG-FPLPWBNLSA-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
PF00165' 'PF22404

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_3233.

PDB 3

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)