Ligand profile

AO3

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

Bound to: VK055_1259 — glycosyl hydrolases 18 family protein

Via homolog PDB 6hm1 UniProt A8GFD6 Formula C₂₅H₄₂N₄O₁₄
Mol. weight 622.63 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AO3
PDB
6hm1
UniProt (similar protein)
A8GFD6
Target protein
VK055_1259

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 622.63 Da
LogP (Crippen) -6.05
H-bond donors 9
H-bond acceptors 16
TPSA 261.56 Ų
Rotatable bonds 9
Aromatic rings 0 / 4
Heavy atoms 43
Fraction sp³ C 0.88
Formula C₂₅H₄₂N₄O₁₄

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 261.6
  • −1 ≤ LogP ≤ 5 -6.05
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 622.6
  • LogP ≤ 5 -6.05
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 16
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 261.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)N[C@@H]1[C@@H]([C@@H]([C@H](O[C@H]1O[C@@H]2[C@H](O[C@H]([C@@H]([C@@H]2O)NC(=O)C)O[C@@H]3[C@H]([C@H]4[C@@H]([C@H]3O)N=C(O4)N(C)C)CO)CO)CO)O)O
InChI 
InChI=1S/C25H42N4O14/c1-8(33)26-14-17(36)16(35)11(6-31)39-23(14)42-22-12(7-32)40-24(15(19(22)38)27-9(2)34)41-21-10(5-30)20-13(18(21)37)28-25(43-20)29(3)4/h10-24,30-32,35-38H,5-7H2,1-4H3,(H,26,33)(H,27,34)/t10-,11+,12+,13+,14+,15+,16+,17-,18+,19-,20-,21+,22+,23-,24-/m0/s1
InChIKey 
MDWNFWDBQGOKNZ-XYUDZHFQSA-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
PF00704

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_1259.

PDB 4

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

Ligand PDB entry

ChEMBL 100

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)