Ligand profile

CB1

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

Bound to: VK055_1987 — oxygen-insensitive NAD(P)H nitroreductase

Via homolog PDB 1idt UniProt P38489 Formula C₉H₈N₄O₅
Mol. weight 252.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CB1
PDB
1idt
UniProt (similar protein)
P38489
Target protein
VK055_1987

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 252.19 Da
LogP (Crippen) 0.42
H-bond donors 1
H-bond acceptors 6
TPSA 132.38 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.22
Formula C₉H₈N₄O₅

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 132.4
  • −1 ≤ LogP ≤ 5 0.42
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 252.2
  • LogP ≤ 5 0.42
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 132.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c(cc(c1N2CC2)[N+](=O)[O-])[N+](=O)[O-])C(=O)N
InChI 
InChI=1S/C9H8N4O5/c10-9(14)5-3-7(11-1-2-11)8(13(17)18)4-6(5)12(15)16/h3-4H,1-2H2,(H2,10,14)
InChIKey 
WOCXQMCIOTUMJV-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
PF00881

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_1987.

PDB 14

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)