Ligand profile

7XP

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

Bound to: VK055_2604 — 16S rRNA m2G1207 methyltransferase

Via homolog PDB 5u0n UniProt Q2MG72 Formula C₁₇H₃₄N₄O₁₀
Mol. weight 454.48 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7XP
PDB
5u0n
UniProt (similar protein)
Q2MG72
Target protein
VK055_2604

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 454.48 Da
LogP (Crippen) -6.65
H-bond donors 10
H-bond acceptors 14
TPSA 262.38 Ų
Rotatable bonds 5
Aromatic rings 0 / 3
Heavy atoms 31
Fraction sp³ C 1.00
Formula C₁₇H₃₄N₄O₁₀

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 262.4
  • −1 ≤ LogP ≤ 5 -6.65
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 454.5
  • LogP ≤ 5 -6.65
  • H-bond donors ≤ 5 10
  • H-bond acceptors ≤ 10 14
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 262.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H](CO2)O)N)O)O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)N)N
InChI 
InChI=1S/C17H34N4O10/c18-4-1-5(19)15(31-17-12(26)8(20)6(23)3-28-17)13(27)14(4)30-16-9(21)11(25)10(24)7(2-22)29-16/h4-17,22-27H,1-3,18-21H2/t4-,5+,6+,7+,8-,9+,10+,11+,12+,13-,14+,15-,16+,17+/m0/s1
InChIKey 
RSLPMOUJEPMGIJ-FHNUIXEPSA-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)