Binder profile

PN5

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

Bound to: PA3454 — acyl-CoA thiolase

Via homolog PDB 2vu2 UniProt P07097 C16H30N2O5S
Mol. weight 362.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PN5
PDB
2vu2
UniProt (similar protein)
P07097
Target protein
PA3454

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 362.49 Da
LogP (Crippen) 0.52
H-bond donors 4
H-bond acceptors 6
TPSA 104.73 Ų
Rotatable bonds 9
Aromatic rings 0 / 0
Heavy atoms 24
Fraction sp³ C 0.81
Formula C16H30N2O5S

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 362.5
  • LogP ≤ 5 0.52
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 104.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)C(=O)OCC(C)(C)[C@H](C(=O)NCCC(=O)NCCS)O
InChI 
InChI=1S/C16H30N2O5S/c1-15(2,3)14(22)23-10-16(4,5)12(20)13(21)18-7-6-11(19)17-8-9-24/h12,20,24H,6-10H2,1-5H3,(H,17,19)(H,18,21)/t12-/m0/s1
InChIKey 
KVQSHCZSRKQWCB-LBPRGKRZSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00108' 'PF02803

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3454.

PDB 10

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)