Ligand profile

ZINC12496578

Virtual-screening candidate from ZINC.

Bound to: KP13_01078 — Penicillin-binding protein activator LpoA

Via homolog UniProt Q7P0B4 Formula C₁₀H₁₇N₃O₆
Tanimoto 0.68
Mol. weight 275.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC12496578
UniProt (similar protein)
Q7P0B4
Tanimoto
0.675
Target protein
KP13_01078

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 275.26 Da
LogP (Crippen) -2.12
H-bond donors 5
H-bond acceptors 5
TPSA 158.82 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 19
Fraction sp³ C 0.60
Formula C₁₀H₁₇N₃O₆

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 158.8
  • −1 ≤ LogP ≤ 5 -2.12
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 275.3
  • LogP ≤ 5 -2.12
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 158.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O
InChI 
InChI=1S/C10H17N3O6/c1-5(9(17)12-4-8(15)16)13-7(14)3-2-6(11)10(18)19/h5-6H,2-4,11H2,1H3,(H,12,17)(H,13,14)(H,15,16)(H,18,19)/t5-,6-/m0/s1
InChIKey 
RPVCUZZJCXVVDW-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
GSH
Homolog
Q7P0B4

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_01078.

PDB 1

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)