Ligand profile

BBP

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

Bound to: VK055_5051 — exonuclease I, 3' -- 5' specific deoxyribophosphodiesterase

Via homolog PDB 3hl8 UniProt P04995 Formula C₁₄H₁₄ClN₃OS
Mol. weight 307.81 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BBP
PDB
3hl8
UniProt (similar protein)
P04995
Target protein
VK055_5051

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 307.81 Da
LogP (Crippen) 4.09
H-bond donors 0
H-bond acceptors 4
TPSA 45.56 Ų
Rotatable bonds 1
Aromatic rings 2 / 3
Heavy atoms 20
Fraction sp³ C 0.36
Formula C₁₄H₁₄ClN₃OS

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 45.6
  • −1 ≤ LogP ≤ 5 4.09
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 307.8
  • LogP ≤ 5 4.09
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 45.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)(C)C1=NN(C(=O)C1)c2nc3ccc(cc3s2)Cl
InChI 
InChI=1S/C14H14ClN3OS/c1-14(2,3)11-7-12(19)18(17-11)13-16-9-5-4-8(15)6-10(9)20-13/h4-6H,7H2,1-3H3
InChIKey 
PZAXHXFHBHHFNG-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
PF08411

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_5051.

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)