Ligand profile

K8M

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

Bound to: VK055_3667 — pirin-like protein

Via homolog PDB 6n0k UniProt O00625 Formula C₂₄H₁₉ClF₃N₃O₂
Mol. weight 473.88 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K8M
PDB
6n0k
UniProt (similar protein)
O00625
Target protein
VK055_3667

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 473.88 Da
LogP (Crippen) 5.28
H-bond donors 1
H-bond acceptors 3
TPSA 62.30 Ų
Rotatable bonds 4
Aromatic rings 3 / 4
Heavy atoms 33
Fraction sp³ C 0.21
Formula C₂₄H₁₉ClF₃N₃O₂

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 62.3
  • −1 ≤ LogP ≤ 5 5.28
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 473.9
  • LogP ≤ 5 5.28
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 62.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1NC(=O)[C@@H]2CC(CN(C2)C(=O)c3cc(cc(c3)F)c4ccncc4)(F)F)Cl
InChI 
InChI=1S/C24H19ClF3N3O2/c25-19-1-3-21(4-2-19)30-22(32)18-12-24(27,28)14-31(13-18)23(33)17-9-16(10-20(26)11-17)15-5-7-29-8-6-15/h1-11,18H,12-14H2,(H,30,32)/t18-/m1/s1
InChIKey 
BEDJWRJGMARXLZ-GOSISDBHSA-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
PF02678' 'PF05726

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_3667.

PDB 4

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

Ligand PDB entry

ChEMBL 10

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)