Ligand profile

PD2

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

Bound to: VK055_1328 — cupin superfamily protein

Via homolog PDB 4diq UniProt Q9H6W3 Formula C₇H₅NO₄
Mol. weight 167.12 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PD2
PDB
4diq
UniProt (similar protein)
Q9H6W3
Target protein
VK055_1328

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 167.12 Da
LogP (Crippen) 0.48
H-bond donors 2
H-bond acceptors 3
TPSA 87.49 Ų
Rotatable bonds 2
Aromatic rings 1 / 1
Heavy atoms 12
Fraction sp³ C 0.00
Formula C₇H₅NO₄

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 87.5
  • −1 ≤ LogP ≤ 5 0.48
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 167.1
  • LogP ≤ 5 0.48
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 3
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 87.5
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cnc(cc1C(=O)O)C(=O)O
InChI 
InChI=1S/C7H5NO4/c9-6(10)4-1-2-8-5(3-4)7(11)12/h1-3H,(H,9,10)(H,11,12)
InChIKey 
MJIVRKPEXXHNJT-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
PF08007

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_1328.

PDB 4

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)