Ligand profile

1X8

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

Bound to: KP13_03557 — DNA ligase

Via homolog PDB 4lh7 UniProt Q837V6 Formula C₉H₈N₄O₂S
Mol. weight 236.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
1X8
PDB
4lh7
UniProt (similar protein)
Q837V6
Target protein
KP13_03557

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 236.26 Da
LogP (Crippen) 0.08
H-bond donors 3
H-bond acceptors 5
TPSA 125.09 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 16
Fraction sp³ C 0.00
Formula C₉H₈N₄O₂S

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 125.1
  • −1 ≤ LogP ≤ 5 0.08
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 236.3
  • LogP ≤ 5 0.08
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 125.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1c2c(c(cnc2N)C(=O)N)sc1C(=O)N
InChI 
InChI=1S/C9H8N4O2S/c10-7-3-1-5(9(12)15)16-6(3)4(2-13-7)8(11)14/h1-2H,(H2,10,13)(H2,11,14)(H2,12,15)
InChIKey 
VOGMWPBBHVVUAW-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
PF01653

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_03557.

PDB 8

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

Ligand PDB entry

ChEMBL 1

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)