Ligand profile

ZVY

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

Bound to: KP13_01350 — Pantothenate kinase

Via homolog PDB 4bfy UniProt P9WPA7 Formula C₂₅H₂₄N₄O₃
Mol. weight 428.49 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZVY
PDB
4bfy
UniProt (similar protein)
P9WPA7
Target protein
KP13_01350

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 428.49 Da
LogP (Crippen) 3.41
H-bond donors 1
H-bond acceptors 6
TPSA 89.69 Ų
Rotatable bonds 7
Aromatic rings 3 / 4
Heavy atoms 32
Fraction sp³ C 0.24
Formula C₂₅H₂₄N₄O₃

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 89.7
  • −1 ≤ LogP ≤ 5 3.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 428.5
  • LogP ≤ 5 3.41
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 89.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccnc(c1)N2CCN(CC2)Cc3cc(ccc3c4ccc(cc4)C#N)OCC(=O)O
InChI 
InChI=1S/C25H24N4O3/c26-16-19-4-6-20(7-5-19)23-9-8-22(32-18-25(30)31)15-21(23)17-28-11-13-29(14-12-28)24-3-1-2-10-27-24/h1-10,15H,11-14,17-18H2,(H,30,31)
InChIKey 
AKNGILSRJWORBU-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
PF00485

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_01350.

PDB 19

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)