Binder profile

B6X

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

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

Via homolog PDB 6j39 UniProt X5IYZ1 C11H20O4S
Mol. weight 248.34 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
B6X
PDB
6j39
UniProt (similar protein)
X5IYZ1
Target protein
PA5304

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 248.34 Da
LogP (Crippen) 2.62
H-bond donors 2
H-bond acceptors 3
TPSA 74.60 Ų
Rotatable bonds 10
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.82
Formula C11H20O4S

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 248.3
  • LogP ≤ 5 2.62
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 10
  • TPSA ≤ 140 Ų 74.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCC[C@H](CC(=O)O)SCC(=O)O
InChI 
InChI=1S/C11H20O4S/c1-2-3-4-5-6-9(7-10(12)13)16-8-11(14)15/h9H,2-8H2,1H3,(H,12,13)(H,14,15)/t9-/m1/s1
InChIKey 
YVPPUISYPJOKND-SECBINFHSA-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
PF01266

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 8

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)