Ligand profile

ZINC2024475

Virtual-screening candidate from ZINC.

Bound to: VK055_4856 — o-succinylbenzoate synthase

Via homolog UniProt Q47Q21 Formula C₁₂H₁₃NO₅
Tanimoto 0.53
Mol. weight 251.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC2024475
UniProt (similar protein)
Q47Q21
Tanimoto
0.529
Target protein
VK055_4856

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 251.24 Da
LogP (Crippen) 0.98
H-bond donors 3
H-bond acceptors 3
TPSA 103.70 Ų
Rotatable bonds 6
Aromatic rings 1 / 1
Heavy atoms 18
Fraction sp³ C 0.25
Formula C₁₂H₁₃NO₅

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 103.7
  • −1 ≤ LogP ≤ 5 0.98
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 251.2
  • LogP ≤ 5 0.98
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 103.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)CCCNC(=O)c1ccccc1C(=O)O
InChI 
InChI=1S/C12H13NO5/c14-10(15)6-3-7-13-11(16)8-4-1-2-5-9(8)12(17)18/h1-2,4-5H,3,6-7H2,(H,13,16)(H,14,15)(H,17,18)
InChIKey 
LENIZMSGCFPTBO-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
OSB
Homolog
Q47Q21

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other ligands for this protein

Quick navigation to other ligands bound to VK055_4856.

PDB 3

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)