Ligand profile

GNB

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

Bound to: KP13_05149 — Lactoylglutathione lyase

Via homolog PDB 1qip UniProt Q04760 Formula C₁₈H₂₄N₄O₁₀S
Mol. weight 488.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GNB
PDB
1qip
UniProt (similar protein)
Q04760
Target protein
KP13_05149

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 488.48 Da
LogP (Crippen) -1.00
H-bond donors 6
H-bond acceptors 10
TPSA 231.42 Ų
Rotatable bonds 15
Aromatic rings 1 / 1
Heavy atoms 33
Fraction sp³ C 0.44
Formula C₁₈H₂₄N₄O₁₀S

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.

  • TPSA ≤ 90 Ų 231.4
  • −1 ≤ LogP ≤ 5 -1.00
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 488.5
  • LogP ≤ 5 -1.00
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 231.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(ccc1COC(O)SC[C@@H](C(=O)NCC(=O)O)NC(=O)CC[C@@H](C(=O)O)N)[N+](=O)[O-]
InChI 
InChI=1S/C18H24N4O10S/c19-12(17(27)28)5-6-14(23)21-13(16(26)20-7-15(24)25)9-33-18(29)32-8-10-1-3-11(4-2-10)22(30)31/h1-4,12-13,18,29H,5-9,19H2,(H,20,26)(H,21,23)(H,24,25)(H,27,28)/t12-,13-,18?/m0/s1
InChIKey 
QYFGPQQSJQOGEO-TVJRNMROSA-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
PF00903

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_05149.

PDB 15

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

Ligand PDB entry

ChEMBL 61

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)