Binder profile

ZINC59703646

Virtual-screening candidate from ZINC.

Bound to: PA5213 — glycine dehydrogenase

Via homolog UniProt Q5SKW8 C8H10O8
Tanimoto 0.50
Mol. weight 234.16 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC59703646
UniProt (similar protein)
Q5SKW8
Tanimoto
0.500
Target protein
PA5213

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 234.16 Da
LogP (Crippen) -0.98
H-bond donors 2
H-bond acceptors 6
TPSA 127.20 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.50
Formula C8H10O8

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 234.2
  • LogP ≤ 5 -0.98
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 127.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)COC(=O)CCC(=O)OCC(=O)O
InChI 
InChI=1S/C8H10O8/c9-5(10)3-15-7(13)1-2-8(14)16-4-6(11)12/h1-4H2,(H,9,10)(H,11,12)
InChIKey 
KMNMWVCPPPTSTP-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal TPW step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
AOA
Homolog
Q5SKW8

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA5213.

PDB 2

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

Ligand PDB entry

ZINC 5

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)