Ligand profile

3J5

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

Bound to: VK055_3566 — ankyrin repeat family protein

Via homolog PDB 4w6e UniProt O95271 Formula C₂₇H₂₉N₅O₂
Mol. weight 455.56 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3J5
PDB
4w6e
UniProt (similar protein)
O95271
Target protein
VK055_3566

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 455.56 Da
LogP (Crippen) 3.59
H-bond donors 2
H-bond acceptors 6
TPSA 85.35 Ų
Rotatable bonds 4
Aromatic rings 4 / 5
Heavy atoms 34
Fraction sp³ C 0.30
Formula C₂₇H₂₉N₅O₂

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 85.3
  • −1 ≤ LogP ≤ 5 3.59
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 455.6
  • LogP ≤ 5 3.59
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 85.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(ncc1c2ccc(cc2)C3=Nc4c(cccc4C(=O)N3)CO)N5CCN([C@H](C5)C)C
InChI 
InChI=1S/C27H29N5O2/c1-17-13-24(32-12-11-31(3)18(2)15-32)28-14-23(17)19-7-9-20(10-8-19)26-29-25-21(16-33)5-4-6-22(25)27(34)30-26/h4-10,13-14,18,33H,11-12,15-16H2,1-3H3,(H,29,30,34)/t18-/m0/s1
InChIKey 
CFSYLGXBPQXCCL-SFHVURJKSA-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
PF00644

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_3566.

PDB 124

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)