Ligand profile

ZINC1730855

Virtual-screening candidate from ZINC.

Bound to: KP13_03557 — DNA ligase

Via homolog UniProt P9WNV1 Formula C₁₈H₂₀N₆
Tanimoto 0.87
Mol. weight 320.40 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1730855
UniProt (similar protein)
P9WNV1
Tanimoto
0.867
Target protein
KP13_03557

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 320.40 Da
LogP (Crippen) 1.60
H-bond donors 4
H-bond acceptors 4
TPSA 81.42 Ų
Rotatable bonds 2
Aromatic rings 3 / 5
Heavy atoms 24
Fraction sp³ C 0.33
Formula C₁₈H₂₀N₆

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 81.4
  • −1 ≤ LogP ≤ 5 1.60
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 320.4
  • LogP ≤ 5 1.60
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 81.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1nc2c([nH]1)CCN[C@H]2c1ccc([C@H]2NCCc3[nH]cnc32)cc1
InChI 
InChI=1S/C18H20N6/c1-2-12(16-18-14(6-8-20-16)22-10-24-18)4-3-11(1)15-17-13(5-7-19-15)21-9-23-17/h1-4,9-10,15-16,19-20H,5-8H2,(H,21,23)(H,22,24)/t15-,16+
InChIKey 
YMRZRVBWYWHBST-IYBDPMFKSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
EWO
Homolog
P9WNV1

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 9

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 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)