Ligand profile

BES

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_03831 — Succinyl-diaminopimelate desuccinylase

Via homolog PDB 4ruh UniProt Q96KP4 Formula C₁₆H₂₄N₂O₄
Mol. weight 308.38 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
BES
PDB
4ruh
UniProt (similar protein)
Q96KP4
Target protein
KP13_03831

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 308.38 Da
LogP (Crippen) 0.53
H-bond donors 4
H-bond acceptors 4
TPSA 112.65 Ų
Rotatable bonds 8
Aromatic rings 1 / 1
Heavy atoms 22
Fraction sp³ C 0.50
Formula C₁₆H₂₄N₂O₄

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 112.7
  • −1 ≤ LogP ≤ 5 0.53
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 308.4
  • LogP ≤ 5 0.53
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 112.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)C[C@@H](C(=O)O)NC(=O)[C@H]([C@@H](Cc1ccccc1)N)O
InChI 
InChI=1S/C16H24N2O4/c1-10(2)8-13(16(21)22)18-15(20)14(19)12(17)9-11-6-4-3-5-7-11/h3-7,10,12-14,19H,8-9,17H2,1-2H3,(H,18,20)(H,21,22)/t12-,13+,14+/m1/s1
InChIKey 
VGGGPCQERPFHOB-RDBSUJKOSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01546' 'PF07687

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 3

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

Ligand PDB entry

ZINC 50

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

Compound Similarity (Tanimoto)