Binder profile

DNO

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

Bound to: PA3454 — acyl-CoA thiolase

Via homolog PDB 2wku UniProt P07097 C6H12O6
Mol. weight 180.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DNO
PDB
2wku
UniProt (similar protein)
P07097
Target protein
PA3454

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 180.16 Da
LogP (Crippen) -3.38
H-bond donors 5
H-bond acceptors 6
TPSA 118.22 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 12
Fraction sp³ C 0.83
Formula C6H12O6

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 180.2
  • LogP ≤ 5 -3.38
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 118.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@H]([C@H]([C@@H]([C@@H](C=O)O)O)O)O)O
InChI 
InChI=1S/C6H12O6/c7-1-3(9)5(11)6(12)4(10)2-8/h1,3-6,8-12H,2H2/t3-,4-,5-,6-/m1/s1
InChIKey 
GZCGUPFRVQAUEE-KVTDHHQDSA-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)