Ligand profile

9W1

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

Bound to: KP13_04751 — Adenosylhomocysteinase

Via homolog PDB 5w49 UniProt P23526 Formula C₂₀H₂₂N₆O₃
Mol. weight 394.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
9W1
PDB
5w49
UniProt (similar protein)
P23526
Target protein
KP13_04751

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 394.44 Da
LogP (Crippen) 2.74
H-bond donors 2
H-bond acceptors 8
TPSA 119.40 Ų
Rotatable bonds 5
Aromatic rings 3 / 4
Heavy atoms 29
Fraction sp³ C 0.30
Formula C₂₀H₂₂N₆O₃

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 119.4
  • −1 ≤ LogP ≤ 5 2.74
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 394.4
  • LogP ≤ 5 2.74
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 119.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(cc(n1)[C@@H]2CCN(C2)C(=O)c3c(non3)N)Nc4cccc(c4)OC
InChI 
InChI=1S/C20H22N6O3/c1-12-8-15(23-14-4-3-5-16(9-14)28-2)10-17(22-12)13-6-7-26(11-13)20(27)18-19(21)25-29-24-18/h3-5,8-10,13H,6-7,11H2,1-2H3,(H2,21,25)(H,22,23)/t13-/m1/s1
InChIKey 
BJUGLSYIEXNITK-CYBMUJFWSA-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)