Ligand profile

RDE

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

Bound to: KP13_32123 — chaperone protein HtpG

Via homolog PDB 1zwh UniProt P02829 Formula C₁₈H₂₀ClNO₇
Mol. weight 397.81 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RDE
PDB
1zwh
UniProt (similar protein)
P02829
Target protein
KP13_32123

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 397.81 Da
LogP (Crippen) 2.76
H-bond donors 3
H-bond acceptors 8
TPSA 120.47 Ų
Rotatable bonds 7
Aromatic rings 2 / 2
Heavy atoms 27
Fraction sp³ C 0.28
Formula C₁₈H₂₀ClNO₇

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 120.5
  • −1 ≤ LogP ≤ 5 2.76
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 397.8
  • LogP ≤ 5 2.76
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 8
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 120.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1cc(c(c(c1OC)CCOC(=O)c2cc(c(cc2O)O)Cl)OC)N
InChI 
InChI=1S/C18H20ClNO7/c1-24-15-7-12(20)16(25-2)9(17(15)26-3)4-5-27-18(23)10-6-11(19)14(22)8-13(10)21/h6-8,21-22H,4-5,20H2,1-3H3
InChIKey 
DFYGLJKFZQGYPA-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
PF02518

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_32123.

PDB 27

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

Ligand PDB entry

ChEMBL 6

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)