Ligand profile

K0D

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

Bound to: KP13_09841 — ADP compounds hydrolase nudE

Via homolog PDB 5qj9 UniProt Q9UKK9 Formula C₉H₁₃N₃O₂S
Mol. weight 227.29 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
K0D
PDB
5qj9
UniProt (similar protein)
Q9UKK9
Target protein
KP13_09841

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 227.29 Da
LogP (Crippen) 0.79
H-bond donors 0
H-bond acceptors 5
TPSA 55.32 Ų
Rotatable bonds 1
Aromatic rings 1 / 2
Heavy atoms 15
Fraction sp³ C 0.67
Formula C₉H₁₃N₃O₂S

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 55.3
  • −1 ≤ LogP ≤ 5 0.79
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 227.3
  • LogP ≤ 5 0.79
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 55.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H]1CN([C@H](CO1)C)C(=O)c2cnsn2
InChI 
InChI=1S/C9H13N3O2S/c1-6-5-14-7(2)4-12(6)9(13)8-3-10-15-11-8/h3,6-7H,4-5H2,1-2H3/t6-,7+/m0/s1
InChIKey 
IKMQGCCZPWFVJE-NKWVEPMBSA-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)