Ligand profile

TFD

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 4iks UniProt P53582 Formula C₁₈H₁₆ClF₃N₆
Mol. weight 408.82 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
TFD
PDB
4iks
UniProt (similar protein)
P53582
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 408.82 Da
LogP (Crippen) 4.44
H-bond donors 2
H-bond acceptors 6
TPSA 75.62 Ų
Rotatable bonds 6
Aromatic rings 3 / 3
Heavy atoms 28
Fraction sp³ C 0.22
Formula C₁₈H₁₆ClF₃N₆

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 75.6
  • −1 ≤ LogP ≤ 5 4.44
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 408.8
  • LogP ≤ 5 4.44
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 75.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1c(c(nc(n1)c2ccccn2)NCCNc3cccc(n3)C(F)(F)F)Cl
InChI 
InChI=1S/C18H16ClF3N6/c1-11-15(19)17(28-16(26-11)12-5-2-3-8-23-12)25-10-9-24-14-7-4-6-13(27-14)18(20,21)22/h2-8H,9-10H2,1H3,(H,24,27)(H,25,26,28)
InChIKey 
BDLJLGRTYOMPEG-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
PF00557

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_2384.

PDB 45

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)