Ligand profile

7QM

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

Bound to: VK055_2604 — 16S rRNA m2G1207 methyltransferase

Via homolog PDB 5u1i UniProt Q2MG72 Formula C₁₉H₃₉N₅O₁₀
Mol. weight 497.55 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7QM
PDB
5u1i
UniProt (similar protein)
Q2MG72
Target protein
VK055_2604

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 497.55 Da
LogP (Crippen) -7.06
H-bond donors 11
H-bond acceptors 15
TPSA 274.41 Ų
Rotatable bonds 7
Aromatic rings 0 / 3
Heavy atoms 34
Fraction sp³ C 1.00
Formula C₁₉H₃₉N₅O₁₀

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 274.4
  • −1 ≤ LogP ≤ 5 -7.06
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 497.5
  • LogP ≤ 5 -7.06
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 15
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 274.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN[C@H]1[C@@H]([C@H](O[C@@H]([C@@H]1O)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)CN)O)O)N)N)N)CO)O
InChI 
InChI=1S/C19H39N5O10/c1-24-10-11(26)8(4-25)32-19(14(10)29)34-17-6(22)2-5(21)16(15(17)30)33-18-9(23)13(28)12(27)7(3-20)31-18/h5-19,24-30H,2-4,20-23H2,1H3/t5-,6+,7+,8+,9+,10-,11+,12+,13+,14+,15-,16+,17-,18+,19+/m0/s1
InChIKey 
DXFGBSJHOFHYGL-OADJNCRJSA-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)