Binder profile

SEC

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

Bound to: PA3667 — cysteine desulfurase

Via homolog PDB 1kmk UniProt P77444 C3H7NO2Se
Mol. weight 168.05 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SEC
PDB
1kmk
UniProt (similar protein)
P77444
Target protein
PA3667

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 168.05 Da
LogP (Crippen) -1.28
H-bond donors 2
H-bond acceptors 2
TPSA 63.32 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 7
Fraction sp³ C 0.67
Formula C3H7NO2Se

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 168.1
  • LogP ≤ 5 -1.28
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 63.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H](C(=O)O)N)[SeH]
InChI 
InChI=1S/C3H7NO2Se/c4-2(1-7)3(5)6/h2,7H,1,4H2,(H,5,6)/t2-/m0/s1
InChIKey 
ZKZBPNGNEQAJSX-REOHCLBHSA-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
PF00266

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA3667.

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)