Ligand profile

ZINC25756940

Virtual-screening candidate from ZINC.

Bound to: KP13_03557 — DNA ligase

Via homolog UniProt Q837V6 Formula C₁₃H₂₀N₂O₆P⁺
Tanimoto 0.76
Mol. weight 331.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC25756940
UniProt (similar protein)
Q837V6
Tanimoto
0.760
Target protein
KP13_03557

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 331.29 Da
LogP (Crippen) 0.35
H-bond donors 3
H-bond acceptors 4
TPSA 122.96 Ų
Rotatable bonds 5
Aromatic rings 1 / 2
Heavy atoms 22
Fraction sp³ C 0.54
Formula C₁₃H₂₀N₂O₆P⁺

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 123.0
  • −1 ≤ LogP ≤ 5 0.35
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 331.3
  • LogP ≤ 5 0.35
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 123.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1[C@@H](COP(=O)(O)O)O[C@@H]([n+]2cccc(C(N)=O)c2)[C@@H]1C
InChI 
InChI=1S/C13H19N2O6P/c1-8-9(2)13(21-11(8)7-20-22(17,18)19)15-5-3-4-10(6-15)12(14)16/h3-6,8-9,11,13H,7H2,1-2H3,(H3-,14,16,17,18,19)/p+1/t8-,9+,11+,13+/m0/s1
InChIKey 
YYNOOWWEYJELSF-SEMCEJNYSA-O

Provenance

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

Method
LigQ nearest_k
Query
NMN
Homolog
Q837V6

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)