Ligand profile

PSU

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

Bound to: VK055_3750 — translation elongation factor Tu

Via homolog PDB 5afi UniProt P0CE48 Formula C₉H₁₃N₂O₉P
Mol. weight 324.18 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PSU
PDB
5afi
UniProt (similar protein)
P0CE48
Target protein
VK055_3750

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 324.18 Da
LogP (Crippen) -2.67
H-bond donors 6
H-bond acceptors 7
TPSA 182.17 Ų
Rotatable bonds 4
Aromatic rings 1 / 2
Heavy atoms 21
Fraction sp³ C 0.56
Formula C₉H₁₃N₂O₉P

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 182.2
  • −1 ≤ LogP ≤ 5 -2.67
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 324.2
  • LogP ≤ 5 -2.67
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 182.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C1=C(C(=O)NC(=O)N1)[C@H]2[C@@H]([C@@H]([C@H](O2)COP(=O)(O)O)O)O
InChI 
InChI=1S/C9H13N2O9P/c12-5-4(2-19-21(16,17)18)20-7(6(5)13)3-1-10-9(15)11-8(3)14/h1,4-7,12-13H,2H2,(H2,16,17,18)(H2,10,11,14,15)/t4-,5-,6-,7+/m1/s1
InChIKey 
MOBMOJGXNHLLIR-GBNDHIKLSA-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
PF00237

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_3750.

PDB 19

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)