Ligand profile

CM5

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

Bound to: KP13_03895 — putative transporter protein

Via homolog PDB 2wsw UniProt B4EY22 Formula C₂₃H₄₂O₁₁
Mol. weight 494.58 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
CM5
PDB
2wsw
UniProt (similar protein)
B4EY22
Target protein
KP13_03895

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 494.58 Da
LogP (Crippen) -1.23
H-bond donors 7
H-bond acceptors 11
TPSA 178.53 Ų
Rotatable bonds 11
Aromatic rings 0 / 3
Heavy atoms 34
Fraction sp³ C 1.00
Formula C₂₃H₄₂O₁₁

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 178.5
  • −1 ≤ LogP ≤ 5 -1.23
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 494.6
  • LogP ≤ 5 -1.23
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 178.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1CCC(CC1)CCCCCO[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O)O)O
InChI 
InChI=1S/C23H42O11/c24-11-14-16(26)17(27)19(29)23(32-14)34-21-15(12-25)33-22(20(30)18(21)28)31-10-6-2-5-9-13-7-3-1-4-8-13/h13-30H,1-12H2/t14-,15-,16-,17+,18-,19-,20-,21-,22-,23-/m1/s1
InChIKey 
RVTGFZGNOSKUDA-ZNGNCRBCSA-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
PF02028

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_03895.

PDB 7

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)