Ligand profile

7VD

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

Bound to: VK055_3929 — 2-hydroxy-3-oxopropionate reductase

Via homolog PDB 5u5g UniProt I6R485 Formula C₃H₇O₄P
Mol. weight 138.06 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
7VD
PDB
5u5g
UniProt (similar protein)
I6R485
Target protein
VK055_3929

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 138.06 Da
LogP (Crippen) -0.25
H-bond donors 2
H-bond acceptors 2
TPSA 74.60 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 8
Fraction sp³ C 0.67
Formula C₃H₇O₄P

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 -0.25
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 138.1
  • LogP ≤ 5 -0.25
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 74.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=O)CP(=O)(O)O
InChI 
InChI=1S/C3H7O4P/c1-3(4)2-8(5,6)7/h2H2,1H3,(H2,5,6,7)
InChIKey 
DVSHXLWNRCEDCW-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
PF03446' 'PF14833

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_3929.

PDB 8

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)