Ligand profile

VI

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

Bound to: VK055_1079 — metallo-beta-lactamase superfamily protein

Via homolog PDB 2gfj UniProt P52700 Formula C₁₇H₁₂N₂O₄
Mol. weight 308.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VI
PDB
2gfj
UniProt (similar protein)
P52700
Target protein
VK055_1079

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 308.29 Da
LogP (Crippen) 2.94
H-bond donors 2
H-bond acceptors 4
TPSA 92.42 Ų
Rotatable bonds 4
Aromatic rings 3 / 3
Heavy atoms 23
Fraction sp³ C 0.00
Formula C₁₇H₁₂N₂O₄

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 92.4
  • −1 ≤ LogP ≤ 5 2.94
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 308.3
  • LogP ≤ 5 2.94
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 92.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1ccc(cc1)c2c(c(n(n2)c3ccccc3)C(=O)O)C(=O)O
InChI 
InChI=1S/C17H12N2O4/c20-16(21)13-14(11-7-3-1-4-8-11)18-19(15(13)17(22)23)12-9-5-2-6-10-12/h1-10H,(H,20,21)(H,22,23)
InChIKey 
WERNQSNSNVDBBJ-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
PF00753

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_1079.

PDB 18

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

Ligand PDB entry

ChEMBL 37

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)