Binder profile

ZINC12496906

Virtual-screening candidate from ZINC.

Bound to: PA5304 — D-amino acid dehydrogenase small subunit

Via homolog UniProt Q50LF2 C20H23N7O6
Tanimoto 0.58
Mol. weight 457.45 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12496906
UniProt (similar protein)
Q50LF2
Tanimoto
0.577
Target protein
PA5304

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 457.45 Da
LogP (Crippen) 0.22
H-bond donors 7
H-bond acceptors 9
TPSA 202.77 Ų
Rotatable bonds 9
Aromatic rings 2 / 3
Heavy atoms 33
Fraction sp³ C 0.25
Formula C20H23N7O6

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 1 violation
  • MW ≤ 500 Da 457.4
  • LogP ≤ 5 0.22
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 202.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1C(CNc2ccc(C(=O)N[C@@H](CCC(=O)O)C(=O)O)cc2)=CNc2[nH]c(N)nc(=O)c21
InChI 
InChI=1S/C20H23N7O6/c1-27-12(9-23-16-15(27)18(31)26-20(21)25-16)8-22-11-4-2-10(3-5-11)17(30)24-13(19(32)33)6-7-14(28)29/h2-5,9,13,22H,6-8H2,1H3,(H,24,30)(H,28,29)(H,32,33)(H4,21,23,25,26,31)/t13-/m0/s1
InChIKey 
VWNDXSYYCICZGD-ZDUSSCGKSA-N

Provenance

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

Method
LigQ nearest_k
Query
FON
Homolog
Q50LF2

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA5304.

PDB 9

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)