Ligand profile

4L9

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

Bound to: VK055_2384 — methionine aminopeptidase, type I

Via homolog PDB 4z7m UniProt P0AE18 Formula C₂₄H₂₅F₂N₃O₃
Mol. weight 441.48 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4L9
PDB
4z7m
UniProt (similar protein)
P0AE18
Target protein
VK055_2384

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 441.48 Da
LogP (Crippen) 2.66
H-bond donors 2
H-bond acceptors 3
TPSA 78.51 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 32
Fraction sp³ C 0.29
Formula C₂₄H₂₅F₂N₃O₃

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 78.5
  • −1 ≤ LogP ≤ 5 2.66
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 441.5
  • LogP ≤ 5 2.66
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 78.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](C(=O)N[C@H]1CC=C[C@@H](N(C1=O)C)c2ccccc2)NC(=O)Cc3cc(cc(c3)F)F
InChI 
InChI=1S/C24H25F2N3O3/c1-15(27-22(30)13-16-11-18(25)14-19(26)12-16)23(31)28-20-9-6-10-21(29(2)24(20)32)17-7-4-3-5-8-17/h3-8,10-12,14-15,20-21H,9,13H2,1-2H3,(H,27,30)(H,28,31)/t15-,20-,21+/m0/s1
InChIKey 
XGCLGFYBNGRVHO-ONGXBYRLSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
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)