Ligand profile

K3D

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

Bound to: KP13_09841 — ADP compounds hydrolase nudE

Via homolog PDB 5qk4 UniProt Q9UKK9 Formula C₉H₁₇N₃O₂
Mol. weight 199.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K3D
PDB
5qk4
UniProt (similar protein)
Q9UKK9
Target protein
KP13_09841

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 199.25 Da
LogP (Crippen) -0.12
H-bond donors 1
H-bond acceptors 2
TPSA 52.65 Ų
Rotatable bonds 1
Aromatic rings 0 / 1
Heavy atoms 14
Fraction sp³ C 0.78
Formula C₉H₁₇N₃O₂

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 52.7
  • −1 ≤ LogP ≤ 5 -0.12
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 199.3
  • LogP ≤ 5 -0.12
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 52.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCNC(=O)N1CCN(CC1)C(=O)C
InChI 
InChI=1S/C9H17N3O2/c1-3-10-9(14)12-6-4-11(5-7-12)8(2)13/h3-7H2,1-2H3,(H,10,14)
InChIKey 
DXJHUMXFQJQTMZ-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)