Ligand profile

ZINC255987062

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q9HT86 Formula C₂₀H₃₆N₆O₈
Tanimoto 0.74
Mol. weight 488.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC255987062
UniProt (similar protein)
Q9HT86
Tanimoto
0.745
Target protein
KP13_01887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 488.54 Da
LogP (Crippen) -2.61
H-bond donors 8
H-bond acceptors 8
TPSA 243.04 Ų
Rotatable bonds 16
Aromatic rings 0 / 0
Heavy atoms 34
Fraction sp³ C 0.70
Formula C₂₀H₃₆N₆O₈

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 243.0
  • −1 ≤ LogP ≤ 5 -2.61
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 488.5
  • LogP ≤ 5 -2.61
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 16
  • TPSA ≤ 140 Ų 243.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](N)C(=O)N[C@H](CCC(=O)N[C@H](CCCCN)C(=O)N[C@@H](C)C(=O)N[C@H](C)C(=O)O)C(=O)O
InChI 
InChI=1S/C20H36N6O8/c1-10(22)16(28)26-14(20(33)34)7-8-15(27)25-13(6-4-5-9-21)18(30)23-11(2)17(29)24-12(3)19(31)32/h10-14H,4-9,21-22H2,1-3H3,(H,23,30)(H,24,29)(H,25,27)(H,26,28)(H,31,32)(H,33,34)/t10-,11-,12+,13+,14+/m0/s1
InChIKey 
MCIBYIIODNXVSL-ODXJTPSBSA-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)