Ligand profile

MDN

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

Bound to: VK055_4487 — alanine--tRNA ligase

Via homolog PDB 3hxy UniProt P00957 Formula CH₆O₆P₂
Mol. weight 176.00 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
MDN
PDB
3hxy
UniProt (similar protein)
P00957
Target protein
VK055_4487

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 176.00 Da
LogP (Crippen) -0.70
H-bond donors 4
H-bond acceptors 2
TPSA 115.06 Ų
Rotatable bonds 2
Aromatic rings 0 / 0
Heavy atoms 9
Fraction sp³ C 1.00
Formula CH₆O₆P₂

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 115.1
  • −1 ≤ LogP ≤ 5 -0.70
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 176.0
  • LogP ≤ 5 -0.70
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 2
Veber's rules Pass
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 115.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C(P(=O)(O)O)P(=O)(O)O
InChI 
InChI=1S/CH6O6P2/c2-8(3,4)1-9(5,6)7/h1H2,(H2,2,3,4)(H2,5,6,7)
InChIKey 
MBKDYNNUVRNNRF-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
PF01411

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_4487.

PDB 6

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)