Ligand profile

HDA

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

Bound to: VK055_2887 — adenylosuccinate synthase

Via homolog PDB 1cg0 UniProt P0A7D4 Formula C₃H₅NO₄
Mol. weight 119.08 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
HDA
PDB
1cg0
UniProt (similar protein)
P0A7D4
Target protein
VK055_2887

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 119.08 Da
LogP (Crippen) -1.08
H-bond donors 2
H-bond acceptors 3
TPSA 77.84 Ų
Rotatable bonds 3
Aromatic rings 0 / 0
Heavy atoms 8
Fraction sp³ C 0.33
Formula C₃H₅NO₄

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 77.8
  • −1 ≤ LogP ≤ 5 -1.08
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 119.1
  • LogP ≤ 5 -1.08
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 77.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(C(=O)O)N(C=O)O
InChI 
InChI=1S/C3H5NO4/c5-2-4(8)1-3(6)7/h2,8H,1H2,(H,6,7)
InChIKey 
URJHVPKUWOUENU-UHFFFAOYSA-N

Provenance

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

Method
LigQ sequence
Source
PDB
Binding sites
PF00709

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_2887.

PDB 14

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)