Ligand profile

O4S

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

Bound to: VK055_3060 — bacterial transferase hexapeptide family protein

Via homolog PDB 6p86 UniProt P21645 Formula C₂₈H₃₄N₄O₃
Mol. weight 474.61 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
O4S
PDB
6p86
UniProt (similar protein)
P21645
Target protein
VK055_3060

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 474.61 Da
LogP (Crippen) 3.51
H-bond donors 1
H-bond acceptors 4
TPSA 72.96 Ų
Rotatable bonds 6
Aromatic rings 2 / 5
Heavy atoms 35
Fraction sp³ C 0.46
Formula C₂₈H₃₄N₄O₃

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 73.0
  • −1 ≤ LogP ≤ 5 3.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 474.6
  • LogP ≤ 5 3.51
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 73.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCc1ccc(cc1)CNC(=O)CN2c3cc(ccc3N4CCCC[C@@H]4C2=O)C(=O)N5CCCC5
InChI 
InChI=1S/C28H34N4O3/c1-2-20-8-10-21(11-9-20)18-29-26(33)19-32-25-17-22(27(34)30-14-5-6-15-30)12-13-23(25)31-16-4-3-7-24(31)28(32)35/h8-13,17,24H,2-7,14-16,18-19H2,1H3,(H,29,33)/t24-/m1/s1
InChIKey 
HPKMORZWWWMLAR-XMMPIXPASA-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
PF00132

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_3060.

PDB 15

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)