Ligand profile

3M9

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

Bound to: VK055_4295 — peptidase M16 inactive domain protein

Via homolog PDB 4re9 UniProt P14735 Formula C₂₄H₂₂FN₅O₃
Mol. weight 447.47 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3M9
PDB
4re9
UniProt (similar protein)
P14735
Target protein
VK055_4295

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 447.47 Da
LogP (Crippen) 3.18
H-bond donors 3
H-bond acceptors 6
TPSA 109.14 Ų
Rotatable bonds 8
Aromatic rings 4 / 4
Heavy atoms 33
Fraction sp³ C 0.17
Formula C₂₄H₂₂FN₅O₃

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 109.1
  • −1 ≤ LogP ≤ 5 3.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 447.5
  • LogP ≤ 5 3.18
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 109.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2cc(ccc2c1)C[C@H](CC(=O)NO)n3c(cnn3)CNC(=O)c4ccc(cc4)F
InChI 
InChI=1S/C24H22FN5O3/c25-20-9-7-18(8-10-20)24(32)26-14-22-15-27-29-30(22)21(13-23(31)28-33)12-16-5-6-17-3-1-2-4-19(17)11-16/h1-11,15,21,33H,12-14H2,(H,26,32)(H,28,31)/t21-/m1/s1
InChIKey 
RJVYTCJRTAVEBT-OAQYLSRUSA-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
PF00675' 'PF05193

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_4295.

PDB 15

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

Ligand PDB entry

ChEMBL 12

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)