Ligand profile

6NM

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

Bound to: VK055_0681 — alpha/beta hydrolase fold family protein

Via homolog PDB 5akh UniProt P34913 Formula C₁₅H₁₀F₃N₃
Mol. weight 289.26 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6NM
PDB
5akh
UniProt (similar protein)
P34913
Target protein
VK055_0681

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 289.26 Da
LogP (Crippen) 4.16
H-bond donors 1
H-bond acceptors 2
TPSA 41.57 Ų
Rotatable bonds 2
Aromatic rings 3 / 3
Heavy atoms 21
Fraction sp³ C 0.07
Formula C₁₅H₁₀F₃N₃

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 41.6
  • −1 ≤ LogP ≤ 5 4.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 289.3
  • LogP ≤ 5 4.16
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 41.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(cc(c1)C(F)(F)F)c2c(cn[nH]2)c3ccncc3
InChI 
InChI=1S/C15H10F3N3/c16-15(17,18)12-3-1-2-11(8-12)14-13(9-20-21-14)10-4-6-19-7-5-10/h1-9H,(H,20,21)
InChIKey 
UZOPNNYVHHABCA-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
PF00561

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_0681.

PDB 98

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)