Ligand profile

ZINC2522687

Virtual-screening candidate from ZINC.

Bound to: KP13_01887 — 1,6-anhydro-N-acetylmuramyl-L-alanine amidase ampD

Via homolog UniProt Q9HT86 Formula C₁₂H₂₃N₃O₄
Tanimoto 0.53
Mol. weight 273.33 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2522687
UniProt (similar protein)
Q9HT86
Tanimoto
0.533
Target protein
KP13_01887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 273.33 Da
LogP (Crippen) -0.55
H-bond donors 4
H-bond acceptors 4
TPSA 121.52 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 19
Fraction sp³ C 0.75
Formula C₁₂H₂₃N₃O₄

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 121.5
  • −1 ≤ LogP ≤ 5 -0.55
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 273.3
  • LogP ≤ 5 -0.55
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 121.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C[C@H](NC(=O)[C@H](C)N)C(=O)N[C@@H](C)C(=O)O
InChI 
InChI=1S/C12H23N3O4/c1-6(2)5-9(15-10(16)7(3)13)11(17)14-8(4)12(18)19/h6-9H,5,13H2,1-4H3,(H,14,17)(H,15,16)(H,18,19)/t7-,8-,9-/m0/s1
InChIKey 
HCZXHQADHZIEJD-CIUDSAMLSA-N

Provenance

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

Method
LigQ nearest_k
Query
J0J
Homolog
Q9HT86

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_01887.

PDB 2

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

Ligand PDB entry

ZINC 45

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

Compound Similarity (Tanimoto)