Ligand profile

SN2

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

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

Via homolog PDB 1oo6 UniProt P38489 Formula C₁₁H₁₂Cl₂N₄O₅
Mol. weight 351.15 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SN2
PDB
1oo6
UniProt (similar protein)
P38489
Target protein
VK055_1987

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 351.15 Da
LogP (Crippen) 1.89
H-bond donors 1
H-bond acceptors 6
TPSA 132.61 Ų
Rotatable bonds 8
Aromatic rings 1 / 1
Heavy atoms 22
Fraction sp³ C 0.36
Formula C₁₁H₁₂Cl₂N₄O₅

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 132.6
  • −1 ≤ LogP ≤ 5 1.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 351.1
  • LogP ≤ 5 1.89
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 132.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c(c(cc(c1N(CCCl)CCCl)[N+](=O)[O-])[N+](=O)[O-])C(=O)N
InChI 
InChI=1S/C11H12Cl2N4O5/c12-1-3-15(4-2-13)9-5-7(11(14)18)8(16(19)20)6-10(9)17(21)22/h5-6H,1-4H2,(H2,14,18)
InChIKey 
DQMALWRRERBILB-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)