Ligand profile

827

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

Bound to: VK055_2604 — 16S rRNA m2G1207 methyltransferase

Via homolog PDB 5u19 UniProt Q2MG72 Formula C₁₉H₃₈N₄O₁₀
Mol. weight 482.53 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
827
PDB
5u19
UniProt (similar protein)
Q2MG72
Target protein
VK055_2604

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 482.53 Da
LogP (Crippen) -6.00
H-bond donors 10
H-bond acceptors 14
TPSA 248.39 Ų
Rotatable bonds 6
Aromatic rings 0 / 3
Heavy atoms 33
Fraction sp³ C 1.00
Formula C₁₉H₃₈N₄O₁₀

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 248.4
  • −1 ≤ LogP ≤ 5 -6.00
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 482.5
  • LogP ≤ 5 -6.00
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 248.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)N)N)N)O
InChI 
InChI=1S/C19H38N4O10/c1-19(29)5-30-18(13(28)16(19)23-2)33-15-7(21)3-6(20)14(12(15)27)32-17-9(22)11(26)10(25)8(4-24)31-17/h6-18,23-29H,3-5,20-22H2,1-2H3/t6-,7+,8+,9+,10+,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1
InChIKey 
HFLKNINDVFJPQT-ZFAMMYHGSA-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
PF05175

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_2604.

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)