Binder profile

2K9

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

Bound to: PA5508 — glutamine synthetase

Via homolog PDB 4xyc UniProt P9WN38 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
PA5508

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.

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 TPW 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 binders for this protein

Quick navigation to other ligands bound to PA5508.

PDB 8

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)