Ligand profile

RD0

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

Bound to: KP13_00305 — Glutathione reductase

Via homolog PDB 6bu7 UniProt Q389T8 Formula C₂₈H₃₈N₄S
Mol. weight 462.71 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RD0
PDB
6bu7
UniProt (similar protein)
Q389T8
Target protein
KP13_00305

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 462.71 Da
LogP (Crippen) 6.41
H-bond donors 1
H-bond acceptors 5
TPSA 33.09 Ų
Rotatable bonds 6
Aromatic rings 3 / 6
Heavy atoms 33
Fraction sp³ C 0.61
Formula C₂₈H₃₈N₄S

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 33.1
  • −1 ≤ LogP ≤ 5 6.41
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 462.7
  • LogP ≤ 5 6.41
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 33.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(ccn2CCC3CCNCC3)cc1c4ncc(s4)C5(CCCCC5)N6CCCC6
InChI 
InChI=1S/C28H38N4S/c1-2-12-28(13-3-1,32-16-4-5-17-32)26-21-30-27(33-26)24-6-7-25-23(20-24)11-19-31(25)18-10-22-8-14-29-15-9-22/h6-7,11,19-22,29H,1-5,8-10,12-18H2
InChIKey 
KBPMYBYNCAAYSC-UHFFFAOYSA-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
PF07992

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_00305.

PDB 23

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

Ligand PDB entry

ChEMBL 2

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)