Binder profile

ADE

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

Bound to: PA3507 — short-chain dehydrogenase

Via homolog PDB 1yxm UniProt Q9BY49 C5H5N5
Mol. weight 135.13 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ADE
PDB
1yxm
UniProt (similar protein)
Q9BY49
Target protein
PA3507

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 135.13 Da
LogP (Crippen) -0.06
H-bond donors 2
H-bond acceptors 4
TPSA 80.48 Ų
Rotatable bonds 0
Aromatic rings 2 / 2
Heavy atoms 10
Fraction sp³ C 0.00
Formula C5H5N5

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 135.1
  • LogP ≤ 5 -0.06
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 80.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1[nH]c2c(n1)c(ncn2)N
InChI 
InChI=1S/C5H5N5/c6-4-3-5(9-1-7-3)10-2-8-4/h1-2H,(H3,6,7,8,9,10)
InChIKey 
GFFGJBXGBJISGV-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
PF13561

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3507.

PDB 7

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)