Ligand profile

DVL

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

Bound to: VK055_0887 — beta-galactosidase

Via homolog PDB 6kuz UniProt P00722 Formula C₂₈H₂₇NO₈S
Mol. weight 537.59 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DVL
PDB
6kuz
UniProt (similar protein)
P00722
Target protein
VK055_0887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 537.59 Da
LogP (Crippen) 2.84
H-bond donors 4
H-bond acceptors 10
TPSA 138.57 Ų
Rotatable bonds 8
Aromatic rings 4 / 5
Heavy atoms 38
Fraction sp³ C 0.29
Formula C₂₈H₂₇NO₈S

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 138.6
  • −1 ≤ LogP ≤ 5 2.84
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 537.6
  • LogP ≤ 5 2.84
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 10
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 138.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(c(c(c1)c2nc3ccccc3s2)OCc4ccc(cc4)O[C@H]5[C@@H]([C@H]([C@H]([C@H](O5)CO)O)O)O)C=O
InChI 
InChI=1S/C28H27NO8S/c1-15-10-17(12-30)26(19(11-15)27-29-20-4-2-3-5-22(20)38-27)35-14-16-6-8-18(9-7-16)36-28-25(34)24(33)23(32)21(13-31)37-28/h2-12,21,23-25,28,31-34H,13-14H2,1H3/t21-,23+,24+,25-,28-/m1/s1
InChIKey 
OIAKZSZIDGSPEQ-WRPMCVFTSA-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
PF00703' 'PF02836' 'PF02837' 'PF02929

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_0887.

PDB 10

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)