Ligand profile

C5J

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

Bound to: KP13_02099 — putative isochorismatase

Via homolog PDB 6xjm UniProt H8ZKV9 Formula C₂H₅N₃O₂
Mol. weight 103.08 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
C5J
PDB
6xjm
UniProt (similar protein)
H8ZKV9
Target protein
KP13_02099

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 103.08 Da
LogP (Crippen) -1.27
H-bond donors 3
H-bond acceptors 2
TPSA 98.21 Ų
Rotatable bonds 0
Aromatic rings 0 / 0
Heavy atoms 7
Fraction sp³ C 0.00
Formula C₂H₅N₃O₂

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 98.2
  • −1 ≤ LogP ≤ 5 -1.27
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 103.1
  • LogP ≤ 5 -1.27
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 0
  • TPSA ≤ 140 Ų 98.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(=O)(N)NC(=O)N
InChI 
InChI=1S/C2H5N3O2/c3-1(6)5-2(4)7/h(H5,3,4,5,6,7)
InChIKey 
OHJMTUPIZMNBFR-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
PF00857

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_02099.

PDB 3

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

Ligand PDB entry

ZINC 8

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)