Ligand profile

AWD

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

Bound to: VK055_0072 — holliday junction DNA helicase RuvB

Via homolog PDB 6g2w UniProt P55072 Formula C₁₂H₁₆FN₃O
Mol. weight 237.28 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AWD
PDB
6g2w
UniProt (similar protein)
P55072
Target protein
VK055_0072

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 237.28 Da
LogP (Crippen) 1.60
H-bond donors 1
H-bond acceptors 2
TPSA 35.58 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 17
Fraction sp³ C 0.42
Formula C₁₂H₁₆FN₃O

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 35.6
  • −1 ≤ LogP ≤ 5 1.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 237.3
  • LogP ≤ 5 1.60
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 35.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CCN(CC1)C(=O)Nc2ccc(cc2)F
InChI 
InChI=1S/C12H16FN3O/c1-15-6-8-16(9-7-15)12(17)14-11-4-2-10(13)3-5-11/h2-5H,6-9H2,1H3,(H,14,17)
InChIKey 
MDBPFVSVLGYVCQ-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
PF00004

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_0072.

PDB 8

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)