Ligand profile

L3B

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

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

Via homolog PDB 5dpx UniProt P52700 Formula C₉H₇N₃S
Mol. weight 189.24 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
L3B
PDB
5dpx
UniProt (similar protein)
P52700
Target protein
VK055_1079

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 189.24 Da
LogP (Crippen) 2.49
H-bond donors 0
H-bond acceptors 2
TPSA 37.08 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 13
Fraction sp³ C 0.11
Formula C₉H₇N₃S

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 37.1
  • −1 ≤ LogP ≤ 5 2.49
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 189.2
  • LogP ≤ 5 2.49
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 37.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccccc1C2=NC(=S)N=N2
InChI 
InChI=1S/C9H7N3S/c1-6-4-2-3-5-7(6)8-10-9(13)12-11-8/h2-5H,1H3
InChIKey 
DEADBTNDSDWXDC-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)