Ligand profile

SAI

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

Bound to: VK055_2341 — methyltransferase domain protein

Via homolog PDB 2avn UniProt Q9X1A9 Formula C₁₄H₂₀N₆O₅Se
Mol. weight 431.31 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
SAI
PDB
2avn
UniProt (similar protein)
Q9X1A9
Target protein
VK055_2341

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 431.31 Da
LogP (Crippen) -1.63
H-bond donors 5
H-bond acceptors 10
TPSA 182.63 Ų
Rotatable bonds 7
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.57
Formula C₁₄H₂₀N₆O₅Se

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 182.6
  • −1 ≤ LogP ≤ 5 -1.63
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 431.3
  • LogP ≤ 5 -1.63
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 182.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)C[Se]CC[C@@H](C(=O)O)N)O)O)N
InChI 
InChI=1S/C14H20N6O5Se/c15-6(14(23)24)1-2-26-3-7-9(21)10(22)13(25-7)20-5-19-8-11(16)17-4-18-12(8)20/h4-7,9-10,13,21-22H,1-3,15H2,(H,23,24)(H2,16,17,18)/t6-,7+,9+,10+,13+/m0/s1
InChIKey 
UVSMMLABJBJNGH-WFMPWKQPSA-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
PF13649

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_2341.

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)