Ligand profile

VC2

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

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

Via homolog PDB 5evd UniProt P52700 Formula C₉H₁₅NO₂S₃
Mol. weight 265.43 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
VC2
PDB
5evd
UniProt (similar protein)
P52700
Target protein
VK055_1079

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 265.43 Da
LogP (Crippen) 1.60
H-bond donors 2
H-bond acceptors 5
TPSA 40.54 Ų
Rotatable bonds 2
Aromatic rings 0 / 2
Heavy atoms 15
Fraction sp³ C 0.89
Formula C₉H₁₅NO₂S₃

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 40.5
  • −1 ≤ LogP ≤ 5 1.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 265.4
  • LogP ≤ 5 1.60
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 40.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC1([C@@H](N2[C@H](S1)CS[C@H]2CS)C(=O)O)C
InChI 
InChI=1S/C9H15NO2S3/c1-9(2)7(8(11)12)10-5(3-13)14-4-6(10)15-9/h5-7,13H,3-4H2,1-2H3,(H,11,12)/t5-,6+,7-/m0/s1
InChIKey 
IKSIYRPSHTUWIX-XVMARJQXSA-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)