Ligand profile

RP7

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

Bound to: VK055_1670 — glycyl radical enzyme, PFL2/glycerol dehydratasefamily protein

Via homolog PDB 6vue UniProt Q30W70 Formula C₆H₁₁NO
Mol. weight 113.16 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RP7
PDB
6vue
UniProt (similar protein)
Q30W70
Target protein
VK055_1670

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 113.16 Da
LogP (Crippen) -0.15
H-bond donors 1
H-bond acceptors 2
TPSA 23.47 Ų
Rotatable bonds 0
Aromatic rings 0 / 1
Heavy atoms 8
Fraction sp³ C 0.67
Formula C₆H₁₁NO

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 23.5
  • −1 ≤ LogP ≤ 5 -0.15
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 113.2
  • LogP ≤ 5 -0.15
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 23.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN1CC=C[C@@H](C1)O
InChI 
InChI=1S/C6H11NO/c1-7-4-2-3-6(8)5-7/h2-3,6,8H,4-5H2,1H3/t6-/m0/s1
InChIKey 
GLDHZKQYHDFALD-LURJTMIESA-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
PF02901

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_1670.

PDB 7

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

Ligand PDB entry

ZINC 21

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

Compound Similarity (Tanimoto)