Ligand profile

K0M

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

Bound to: KP13_09841 — ADP compounds hydrolase nudE

Via homolog PDB 5qjd UniProt Q9UKK9 Formula C₉H₁₀N₄O₂
Mol. weight 206.21 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K0M
PDB
5qjd
UniProt (similar protein)
Q9UKK9
Target protein
KP13_09841

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 206.21 Da
LogP (Crippen) 0.97
H-bond donors 1
H-bond acceptors 5
TPSA 72.95 Ų
Rotatable bonds 2
Aromatic rings 2 / 2
Heavy atoms 15
Fraction sp³ C 0.22
Formula C₉H₁₀N₄O₂

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 73.0
  • −1 ≤ LogP ≤ 5 0.97
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 206.2
  • LogP ≤ 5 0.97
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 73.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
Cc1cc(on1)C(=O)Nc2ccn(n2)C
InChI 
InChI=1S/C9H10N4O2/c1-6-5-7(15-12-6)9(14)10-8-3-4-13(2)11-8/h3-5H,1-2H3,(H,10,11,14)
InChIKey 
DMCIRIFKONIQNK-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
PF00293

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_09841.

PDB 53

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

Ligand PDB entry

ChEMBL 5

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)