Ligand profile

NHP

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

Bound to: KP13_05358 — Tryptophan synthase beta chain

Via homolog PDB 1cx9 UniProt P0A2K1 Formula C₁₀H₁₆NO₃PS
Mol. weight 261.28 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
NHP
PDB
1cx9
UniProt (similar protein)
P0A2K1
Target protein
KP13_05358

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 261.28 Da
LogP (Crippen) 2.32
H-bond donors 3
H-bond acceptors 3
TPSA 83.55 Ų
Rotatable bonds 6
Aromatic rings 1 / 1
Heavy atoms 16
Fraction sp³ C 0.40
Formula C₁₀H₁₆NO₃PS

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.

  • TPSA ≤ 90 Ų 83.6
  • −1 ≤ LogP ≤ 5 2.32
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 261.3
  • LogP ≤ 5 2.32
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 83.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(c(c1)N)SCCCCP(=O)(O)O
InChI 
InChI=1S/C10H16NO3PS/c11-9-5-1-2-6-10(9)16-8-4-3-7-15(12,13)14/h1-2,5-6H,3-4,7-8,11H2,(H2,12,13,14)
InChIKey 
POZPBCXLYRZUTO-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00290

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to KP13_05358.

PDB 40

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)