Ligand profile

ZINC4096970

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q9HT86 Formula C₁₅H₂₃N₃O₁₀
Tanimoto 0.55
Mol. weight 405.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4096970
UniProt (similar protein)
Q9HT86
Tanimoto
0.545
Target protein
KP13_01887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 405.36 Da
LogP (Crippen) -2.04
H-bond donors 7
H-bond acceptors 7
TPSA 233.42 Ų
Rotatable bonds 14
Aromatic rings 0 / 0
Heavy atoms 28
Fraction sp³ C 0.60
Formula C₁₅H₂₃N₃O₁₀

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 233.4
  • −1 ≤ LogP ≤ 5 -2.04
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 405.4
  • LogP ≤ 5 -2.04
  • H-bond donors ≤ 5 7
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 14
  • TPSA ≤ 140 Ų 233.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O)C(=O)O
InChI 
InChI=1S/C15H23N3O10/c16-7(13(23)24)1-4-10(19)17-8(14(25)26)2-5-11(20)18-9(15(27)28)3-6-12(21)22/h7-9H,1-6,16H2,(H,17,19)(H,18,20)(H,21,22)(H,23,24)(H,25,26)(H,27,28)/t7-,8-,9-/m0/s1
InChIKey 
PDMYLTCOWSWSJC-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)