Ligand profile

VDM

Bioactivity hit from ChEMBL on a similar protein.

Bound to: KP13_00302 — Cytoplasmic trehalase

Via homolog UniProt O70282 Formula C₁₄H₂₅NO₈
pchembl 8.31 ~4.9 nM
Mol. weight 335.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VDM
UniProt (similar protein)
O70282
pchembl
8.310 (~4.9 nM)
Target protein
KP13_00302

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 335.35 Da
LogP (Crippen) -4.58
H-bond donors 9
H-bond acceptors 9
TPSA 173.87 Ų
Rotatable bonds 4
Aromatic rings 0 / 2
Heavy atoms 23
Fraction sp³ C 0.86
Formula C₁₄H₂₅NO₈

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 173.9
  • −1 ≤ LogP ≤ 5 -4.58
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 335.4
  • LogP ≤ 5 -4.58
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 173.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@@H]([C@H]([C@H]1N[C@H]2C=C([C@H]([C@@H]([C@H]2O)O)O)CO)O)O)O)CO
InChI 
InChI=1S/C14H25NO8/c16-3-5-1-7(11(20)13(22)9(5)18)15-8-2-6(4-17)10(19)14(23)12(8)21/h1,6-23H,2-4H2/t6-,7+,8+,9-,10-,11+,12+,13+,14+/m1/s1
InChIKey 
YCJYNBLLJHFIIW-MBABXGOBSA-N

Provenance

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

Method
LigQ nearest_k
Source
ChEMBL
Binding sites
PF01204

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_00302.

PDB 1

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 7

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

Compound Similarity (Tanimoto)