Ligand profile

2PV

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

Bound to: KP13_02076 — Nuclease sbcCD subunit D

Via homolog PDB 4o5g UniProt Q9X1X0 Formula C₁₀H₉N₃OS
Mol. weight 219.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
2PV
PDB
4o5g
UniProt (similar protein)
Q9X1X0
Target protein
KP13_02076

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 219.27 Da
LogP (Crippen) 1.41
H-bond donors 3
H-bond acceptors 4
TPSA 78.97 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 15
Fraction sp³ C 0.00
Formula C₁₀H₉N₃OS

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 79.0
  • −1 ≤ LogP ≤ 5 1.41
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 219.3
  • LogP ≤ 5 1.41
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 79.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C\1/NC(=O)/C(=C\c2ccc(cc2)N)/S1
InChI 
InChI=1S/C10H9N3OS/c11-7-3-1-6(2-4-7)5-8-9(14)13-10(12)15-8/h1-5H,11H2,(H2,12,13,14)/b8-5+
InChIKey 
QXOIZYPBCJHYLN-VMPITWQZSA-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
PF00149

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to KP13_02076.

PDB 6

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)