Ligand profile

ZINC2384788

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q9HT86 Formula C₁₁H₂₀N₂O₅
Tanimoto 0.50
Mol. weight 260.29 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2384788
UniProt (similar protein)
Q9HT86
Tanimoto
0.500
Target protein
KP13_01887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 260.29 Da
LogP (Crippen) -0.21
H-bond donors 4
H-bond acceptors 4
TPSA 129.72 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 18
Fraction sp³ C 0.73
Formula C₁₁H₂₀N₂O₅

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 129.7
  • −1 ≤ LogP ≤ 5 -0.21
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 260.3
  • LogP ≤ 5 -0.21
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 129.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O
InChI 
InChI=1S/C11H20N2O5/c1-6(2)5-8(11(17)18)13-9(14)4-3-7(12)10(15)16/h6-8H,3-5,12H2,1-2H3,(H,13,14)(H,15,16)(H,17,18)/t7-,8-/m0/s1
InChIKey 
MYFMARDICOWMQP-YUMQZZPRSA-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)