Ligand profile

AZ1

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

Bound to: VK055_4273 — diaminopimelate decarboxylase

Via homolog PDB 1tuf UniProt Q58497 Formula C₉H₁₆O₄
Mol. weight 188.22 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
AZ1
PDB
1tuf
UniProt (similar protein)
Q58497
Target protein
VK055_4273

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 188.22 Da
LogP (Crippen) 1.89
H-bond donors 2
H-bond acceptors 2
TPSA 74.60 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.78
Formula C₉H₁₆O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 74.6
  • −1 ≤ LogP ≤ 5 1.89
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 188.2
  • LogP ≤ 5 1.89
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 74.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(CCCC(=O)O)CCCC(=O)O
InChI 
InChI=1S/C9H16O4/c10-8(11)6-4-2-1-3-5-7-9(12)13/h1-7H2,(H,10,11)(H,12,13)
InChIKey 
BDJRBEYXGGNYIS-UHFFFAOYSA-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
PF00278' 'PF02784

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_4273.

PDB 5

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)