Ligand profile

9W4

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

Bound to: KP13_04751 — Adenosylhomocysteinase

Via homolog PDB 5w4b UniProt P23526 Formula C₂₂H₁₉N₅O₄S
Mol. weight 449.49 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9W4
PDB
5w4b
UniProt (similar protein)
P23526
Target protein
KP13_04751

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 449.49 Da
LogP (Crippen) 2.92
H-bond donors 1
H-bond acceptors 7
TPSA 104.20 Ų
Rotatable bonds 5
Aromatic rings 3 / 5
Heavy atoms 32
Fraction sp³ C 0.23
Formula C₂₂H₁₉N₅O₄S

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 104.2
  • −1 ≤ LogP ≤ 5 2.92
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 449.5
  • LogP ≤ 5 2.92
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 104.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1CN2C(=O)C=NC2=O)C(=O)Nc3ccc4c(c3)sc(n4)N5CCOCC5
InChI 
InChI=1S/C22H19N5O4S/c28-19-12-23-21(30)27(19)13-14-1-3-15(4-2-14)20(29)24-16-5-6-17-18(11-16)32-22(25-17)26-7-9-31-10-8-26/h1-6,11-12H,7-10,13H2,(H,24,29)
InChIKey 
DIGDPYANABPQFC-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
PF00670' 'PF05221

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_04751.

PDB 6

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)