Ligand profile

ZINC13514803

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q9HT86 Formula C₁₃H₂₁N₃O₈
Tanimoto 0.67
Mol. weight 347.32 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13514803
UniProt (similar protein)
Q9HT86
Tanimoto
0.667
Target protein
KP13_01887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 347.32 Da
LogP (Crippen) -1.88
H-bond donors 6
H-bond acceptors 6
TPSA 196.12 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 24
Fraction sp³ C 0.62
Formula C₁₃H₂₁N₃O₈

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 196.1
  • −1 ≤ LogP ≤ 5 -1.88
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 347.3
  • LogP ≤ 5 -1.88
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 196.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O)C(=O)O
InChI 
InChI=1S/C13H21N3O8/c1-6(11(19)20)15-9(17)5-3-8(13(23)24)16-10(18)4-2-7(14)12(21)22/h6-8H,2-5,14H2,1H3,(H,15,17)(H,16,18)(H,19,20)(H,21,22)(H,23,24)/t6-,7-,8-/m0/s1
InChIKey 
ZIQDDBGXXQXESG-FXQIFTODSA-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)