Ligand profile

ZINC13507523

Virtual-screening candidate from ZINC.

Bound to: KP13_01078 — Penicillin-binding protein activator LpoA

Via homolog UniProt Q7P0B4 Formula C₁₂H₂₁N₃O₆
Tanimoto 0.64
Mol. weight 303.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13507523
UniProt (similar protein)
Q7P0B4
Tanimoto
0.643
Target protein
KP13_01078

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 303.32 Da
LogP (Crippen) -1.48
H-bond donors 5
H-bond acceptors 5
TPSA 158.82 Ų
Rotatable bonds 9
Aromatic rings 0 / 0
Heavy atoms 21
Fraction sp³ C 0.67
Formula C₁₂H₂₁N₃O₆

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 158.8
  • −1 ≤ LogP ≤ 5 -1.48
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 303.3
  • LogP ≤ 5 -1.48
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 158.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
InChI 
InChI=1S/C12H21N3O6/c1-6(2)10(11(19)14-5-9(17)18)15-8(16)4-3-7(13)12(20)21/h6-7,10H,3-5,13H2,1-2H3,(H,14,19)(H,15,16)(H,17,18)(H,20,21)/t7-,10-/m0/s1
InChIKey 
HJXBLWNEFLKSSL-XVKPBYJWSA-N

Provenance

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

Method
LigQ nearest_k
Query
GSH
Homolog
Q7P0B4

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_01078.

PDB 1

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

Ligand PDB entry

ZINC 49

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

Compound Similarity (Tanimoto)