Ligand profile

O3D

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

Bound to: KP13_31828 — UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--2, 6-diaminopimelate ligase

Via homolog PDB 7b60 UniProt P22188 Formula C₉H₁₃NO₃S
Mol. weight 215.27 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
O3D
PDB
7b60
UniProt (similar protein)
P22188
Target protein
KP13_31828

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 215.27 Da
LogP (Crippen) 0.51
H-bond donors 0
H-bond acceptors 4
TPSA 50.52 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 14
Fraction sp³ C 0.56
Formula C₉H₁₃NO₃S

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 50.5
  • −1 ≤ LogP ≤ 5 0.51
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 215.3
  • LogP ≤ 5 0.51
  • H-bond donors ≤ 5 0
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 50.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc(oc1)CN2CCS(=O)(=O)CC2
InChI 
InChI=1S/C9H13NO3S/c11-14(12)6-3-10(4-7-14)8-9-2-1-5-13-9/h1-2,5H,3-4,6-8H2
InChIKey 
AEOGPIJVSQTAII-UHFFFAOYSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Source
PDB
Binding sites
PF02875' 'PF08245

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_31828.

PDB 17

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

Ligand PDB entry

ChEMBL 9

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)