Ligand profile

YT5

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

Bound to: VK055_2367 — acetyl-CoA carboxylase, carboxyl transferase, alpha subunit

Via homolog PDB 5kdr UniProt Q2FXM7 Formula C₂₅H₃₁N₃O₅
Mol. weight 453.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
YT5
PDB
5kdr
UniProt (similar protein)
Q2FXM7
Target protein
VK055_2367

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 453.54 Da
LogP (Crippen) 1.98
H-bond donors 3
H-bond acceptors 5
TPSA 121.44 Ų
Rotatable bonds 10
Aromatic rings 1 / 2
Heavy atoms 33
Fraction sp³ C 0.40
Formula C₂₅H₃₁N₃O₅

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 121.4
  • −1 ≤ LogP ≤ 5 1.98
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 453.5
  • LogP ≤ 5 1.98
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 121.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C/C=C/C=C/C(=O)N[C@@H](CC(=O)N[C@@H](C(C)C)C(=O)[C@H]1[C@@H](C(=O)NC1=O)C)c2ccccc2
InChI 
InChI=1S/C25H31N3O5/c1-5-6-8-13-19(29)26-18(17-11-9-7-10-12-17)14-20(30)27-22(15(2)3)23(31)21-16(4)24(32)28-25(21)33/h5-13,15-16,18,21-22H,14H2,1-4H3,(H,26,29)(H,27,30)(H,28,32,33)/b6-5+,13-8+/t16-,18-,21+,22-/m0/s1
InChIKey 
WMLLJSBRSSYYPT-PQUJRENYSA-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
PF01039

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_2367.

PDB 3

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

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)