Ligand profile

6BV

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

Bound to: KP13_03192 — Periplasmic beta-glucosidase

Via homolog PDB 6lc5 UniProt Q9XEI3 Formula C₁₂H₂₂O₁₀S
Mol. weight 358.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
6BV
PDB
6lc5
UniProt (similar protein)
Q9XEI3
Target protein
KP13_03192

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 358.37 Da
LogP (Crippen) -4.68
H-bond donors 8
H-bond acceptors 11
TPSA 180.30 Ų
Rotatable bonds 4
Aromatic rings 0 / 2
Heavy atoms 23
Fraction sp³ C 1.00
Formula C₁₂H₂₂O₁₀S

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 180.3
  • −1 ≤ LogP ≤ 5 -4.68
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 358.4
  • LogP ≤ 5 -4.68
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 180.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]1[C@H]([C@@H]([C@H]([C@@H](O1)O)O)S[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)O)O
InChI 
InChI=1S/C12H22O10S/c13-1-3-5(15)7(17)8(18)12(22-3)23-10-6(16)4(2-14)21-11(20)9(10)19/h3-20H,1-2H2/t3-,4-,5-,6-,7+,8-,9-,10+,11-,12+/m1/s1
InChIKey 
XRTVCRDMGYFFNB-CSOAUFAESA-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
PF00933

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_03192.

PDB 3

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

Ligand PDB entry

ChEMBL 1

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)