Ligand profile

3R2

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

Bound to: VK055_5103 — Putative UDP-glucoronosyl and UDP-glucosyl transferase

Via homolog PDB 4rif UniProt Q9ZGC0 Formula C₁₇H₂₈N₂O₁₃P₂
Mol. weight 530.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
3R2
PDB
4rif
UniProt (similar protein)
Q9ZGC0
Target protein
VK055_5103

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 530.36 Da
LogP (Crippen) -0.74
H-bond donors 6
H-bond acceptors 12
TPSA 227.07 Ų
Rotatable bonds 8
Aromatic rings 1 / 3
Heavy atoms 34
Fraction sp³ C 0.76
Formula C₁₇H₂₈N₂O₁₃P₂

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 227.1
  • −1 ≤ LogP ≤ 5 -0.74
Lipinski's Rule of Five Fail 3 violations
  • MW ≤ 500 Da 530.4
  • LogP ≤ 5 -0.74
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 227.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H]1C[C@@H](C[C@H]([C@@H]1O)O)OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H](C[C@@H](O2)N3C=C(C(=O)NC3=O)C)O
InChI 
InChI=1S/C17H28N2O13P2/c1-8-3-10(4-12(21)15(8)22)31-34(27,28)32-33(25,26)29-7-13-11(20)5-14(30-13)19-6-9(2)16(23)18-17(19)24/h6,8,10-15,20-22H,3-5,7H2,1-2H3,(H,25,26)(H,27,28)(H,18,23,24)/t8-,10-,11-,12+,13+,14+,15+/m0/s1
InChIKey 
CWVOKCJHBPKJQP-PVMIAKCWSA-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
PF06722' 'PF21036

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_5103.

PDB 4

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)