Ligand profile

ZINC13514809

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q9HT86 Formula C₁₆H₂₈N₄O₈
Tanimoto 0.57
Mol. weight 404.42 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13514809
UniProt (similar protein)
Q9HT86
Tanimoto
0.565
Target protein
KP13_01887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 404.42 Da
LogP (Crippen) -1.77
H-bond donors 7
H-bond acceptors 7
TPSA 222.14 Ų
Rotatable bonds 15
Aromatic rings 0 / 0
Heavy atoms 28
Fraction sp³ C 0.69
Formula C₁₆H₂₈N₄O₈

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 222.1
  • −1 ≤ LogP ≤ 5 -1.77
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 404.4
  • LogP ≤ 5 -1.77
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 15
  • TPSA ≤ 140 Ų 222.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NCCCC[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/C16H28N4O8/c17-8-2-1-3-10(15(25)26)19-13(22)7-5-11(16(27)28)20-12(21)6-4-9(18)14(23)24/h9-11H,1-8,17-18H2,(H,19,22)(H,20,21)(H,23,24)(H,25,26)(H,27,28)/t9-,10-,11-/m0/s1
InChIKey 
ALSOBLJLPFYJBR-DCAQKATOSA-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)