Ligand profile

2K9

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

Bound to: VK055_3295 — glutamine synthetase, type I

Via homolog PDB 4xyc UniProt P9WN38 Formula C₁₉H₁₁N₃O
Mol. weight 297.32 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2K9
PDB
4xyc
UniProt (similar protein)
P9WN38
Target protein
VK055_3295

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 297.32 Da
LogP (Crippen) 2.28
H-bond donors 0
H-bond acceptors 4
TPSA 47.26 Ų
Rotatable bonds 1
Aromatic rings 4 / 5
Heavy atoms 23
Fraction sp³ C 0.00
Formula C₁₉H₁₁N₃O

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 47.3
  • −1 ≤ LogP ≤ 5 2.28
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 297.3
  • LogP ≤ 5 2.28
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 47.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)c2cccc3c2C=C4C3=NC(=O)c5n4ccn5
InChI 
InChI=1S/C19H11N3O/c23-19-18-20-9-10-22(18)16-11-15-13(12-5-2-1-3-6-12)7-4-8-14(15)17(16)21-19/h1-11H
InChIKey 
SFZNDQGUHVYHPD-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
PF00120

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_3295.

PDB 9

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

Ligand PDB entry

ChEMBL 2

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)