Ligand profile

G1L

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

Bound to: VK055_2233 — D-alanine-D-alanine ligase A

Via homolog PDB 2i80 UniProt Q5HEB7 Formula C₁₂H₁₃ClF₃NO
Mol. weight 279.69 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
G1L
PDB
2i80
UniProt (similar protein)
Q5HEB7
Target protein
VK055_2233

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 279.69 Da
LogP (Crippen) 3.91
H-bond donors 1
H-bond acceptors 1
TPSA 29.10 Ų
Rotatable bonds 3
Aromatic rings 1 / 1
Heavy atoms 18
Fraction sp³ C 0.42
Formula C₁₂H₁₃ClF₃NO

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 29.1
  • −1 ≤ LogP ≤ 5 3.91
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 279.7
  • LogP ≤ 5 3.91
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 29.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(CCl)C(=O)Nc1ccc(cc1)C(F)(F)F
InChI 
InChI=1S/C12H13ClF3NO/c1-11(2,7-13)10(18)17-9-5-3-8(4-6-9)12(14,15)16/h3-6H,7H2,1-2H3,(H,17,18)
InChIKey 
QCQZFHOGRCQNIH-UHFFFAOYSA-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
PF01820' 'PF07478

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_2233.

PDB 3

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)