Ligand profile

DKR

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

Bound to: KP13_03557 — DNA ligase

Via homolog PDB 6kkv UniProt P9WNV1 Formula C₁₃H₁₄N₂O
Mol. weight 214.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
DKR
PDB
6kkv
UniProt (similar protein)
P9WNV1
Target protein
KP13_03557

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 214.27 Da
LogP (Crippen) 2.25
H-bond donors 2
H-bond acceptors 1
TPSA 44.89 Ų
Rotatable bonds 3
Aromatic rings 2 / 2
Heavy atoms 16
Fraction sp³ C 0.15
Formula C₁₃H₁₄N₂O

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 44.9
  • −1 ≤ LogP ≤ 5 2.25
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 214.3
  • LogP ≤ 5 2.25
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 1
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 44.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1ccc(cc1)CNC(=O)c2ccc[nH]2
InChI 
InChI=1S/C13H14N2O/c1-10-4-6-11(7-5-10)9-15-13(16)12-3-2-8-14-12/h2-8,14H,9H2,1H3,(H,15,16)
InChIKey 
QNGNTDZXTCCSEP-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
PF22745

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)