Ligand profile

ZINC2579085

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q9HT86 Formula C₉H₁₉N₅O₃
Tanimoto 0.52
Mol. weight 245.28 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2579085
UniProt (similar protein)
Q9HT86
Tanimoto
0.521
Target protein
KP13_01887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 245.28 Da
LogP (Crippen) -1.83
H-bond donors 6
H-bond acceptors 4
TPSA 154.32 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 17
Fraction sp³ C 0.67
Formula C₉H₁₉N₅O₃

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 154.3
  • −1 ≤ LogP ≤ 5 -1.83
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 245.3
  • LogP ≤ 5 -1.83
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 154.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](N)C(=O)N[C@@H](CCCNC(=N)N)C(=O)O
InChI 
InChI=1S/C9H19N5O3/c1-5(10)7(15)14-6(8(16)17)3-2-4-13-9(11)12/h5-6H,2-4,10H2,1H3,(H,14,15)(H,16,17)(H4,11,12,13)/t5-,6-/m0/s1
InChIKey 
SITWEMZOJNKJCH-WDSKDSINSA-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)