Ligand profile

ZINC17125733

Virtual-screening candidate from ZINC.

Bound to: KP13_03831 — Succinyl-diaminopimelate desuccinylase

Via homolog UniProt Q96KP4 Formula C₁₆H₂₄N₂O₅
Tanimoto 0.81
Mol. weight 324.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC17125733
UniProt (similar protein)
Q96KP4
Tanimoto
0.810
Target protein
KP13_03831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 324.38 Da
LogP (Crippen) 0.24
H-bond donors 5
H-bond acceptors 5
TPSA 132.88 Ų
Rotatable bonds 8
Aromatic rings 1 / 1
Heavy atoms 23
Fraction sp³ C 0.50
Formula C₁₆H₂₄N₂O₅

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 132.9
  • −1 ≤ LogP ≤ 5 0.24
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 324.4
  • LogP ≤ 5 0.24
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 5
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 132.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C[C@H](NC(=O)[C@H](O)[C@@H](N)Cc1ccc(O)cc1)C(=O)O
InChI 
InChI=1S/C16H24N2O5/c1-9(2)7-13(16(22)23)18-15(21)14(20)12(17)8-10-3-5-11(19)6-4-10/h3-6,9,12-14,19-20H,7-8,17H2,1-2H3,(H,18,21)(H,22,23)/t12-,13-,14+/m0/s1
InChIKey 
FRMXVEDKXFUWRZ-MELADBBJSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ nearest_k
Query
BES
Homolog
Q96KP4

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_03831.

PDB 4

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)