Ligand profile

3TH

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

Bound to: KP13_00667 — Glycogen phosphorylase

Via homolog PDB 2gm9 UniProt P00489 Formula C₁₆H₁₂ClN₃O₂S
Mol. weight 345.81 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3TH
PDB
2gm9
UniProt (similar protein)
P00489
Target protein
KP13_00667

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 345.81 Da
LogP (Crippen) 3.18
H-bond donors 3
H-bond acceptors 3
TPSA 73.99 Ų
Rotatable bonds 2
Aromatic rings 3 / 4
Heavy atoms 23
Fraction sp³ C 0.12
Formula C₁₆H₁₂ClN₃O₂S

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 74.0
  • −1 ≤ LogP ≤ 5 3.18
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 345.8
  • LogP ≤ 5 3.18
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 74.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc2c(c1)C[C@H](C(=O)N2)NC(=O)c3cc4cc(sc4[nH]3)Cl
InChI 
InChI=1S/C16H12ClN3O2S/c17-13-7-9-6-12(20-16(9)23-13)15(22)19-11-5-8-3-1-2-4-10(8)18-14(11)21/h1-4,6-7,11,20H,5H2,(H,18,21)(H,19,22)/t11-/m1/s1
InChIKey 
LJAHIGGEXIWVJG-LLVKDONJSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF00343

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_00667.

PDB 115

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

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)