Ligand profile

3CU

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

Bound to: KP13_01544 — Periplasmic trehalase

Via homolog PDB 2jjb UniProt P13482 Formula C₈H₁₅NO₅
Mol. weight 205.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3CU
PDB
2jjb
UniProt (similar protein)
P13482
Target protein
KP13_01544

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 205.21 Da
LogP (Crippen) -3.51
H-bond donors 5
H-bond acceptors 6
TPSA 104.39 Ų
Rotatable bonds 1
Aromatic rings 0 / 2
Heavy atoms 14
Fraction sp³ C 1.00
Formula C₈H₁₅NO₅

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 104.4
  • −1 ≤ LogP ≤ 5 -3.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 205.2
  • LogP ≤ 5 -3.51
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 6
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 104.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@H]2[N@@]1[C@@H]([C@H]([C@@H]2O)O)CO)O)O
InChI 
InChI=1S/C8H15NO5/c10-2-3-6(12)8(14)5-7(13)4(11)1-9(3)5/h3-8,10-14H,1-2H2/t3-,4+,5-,6-,7-,8-/m1/s1
InChIKey 
AXTGOJVKRHFYBT-XAZAIFFQSA-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
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_01544.

PDB 1

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

Ligand PDB entry

ChEMBL 3

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 10

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

Compound Similarity (Tanimoto)