Ligand profile

R7M

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

Bound to: VK055_1552 — formate transporter FocA

Via homolog PDB 6vqr UniProt O77389 Formula C₁₂H₉F₅O₄
Mol. weight 312.19 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
R7M
PDB
6vqr
UniProt (similar protein)
O77389
Target protein
VK055_1552

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 312.19 Da
LogP (Crippen) 2.55
H-bond donors 1
H-bond acceptors 4
TPSA 55.76 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 21
Fraction sp³ C 0.42
Formula C₁₂H₉F₅O₄

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 55.8
  • −1 ≤ LogP ≤ 5 2.55
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 312.2
  • LogP ≤ 5 2.55
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 55.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COc1ccc2c(c1)O[C@](CC2=O)(C(C(F)(F)F)(F)F)O
InChI 
InChI=1S/C12H9F5O4/c1-20-6-2-3-7-8(18)5-10(19,21-9(7)4-6)11(13,14)12(15,16)17/h2-4,19H,5H2,1H3/t10-/m1/s1
InChIKey 
NQJASZMLBMBHRG-SNVBAGLBSA-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
PF01226

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_1552.

PDB 1

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)