Ligand profile

4D4

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

Bound to: VK055_3765 — ribosomal protein L14

Via homolog PDB 5it8 UniProt P0ADY3 Formula C₆H₁₄N₄O₃
Mol. weight 190.20 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
4D4
PDB
5it8
UniProt (similar protein)
P0ADY3
Target protein
VK055_3765

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 190.20 Da
LogP (Crippen) -2.37
H-bond donors 6
H-bond acceptors 4
TPSA 145.45 Ų
Rotatable bonds 5
Aromatic rings 0 / 0
Heavy atoms 13
Fraction sp³ C 0.67
Formula C₆H₁₄N₄O₃

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 145.4
  • −1 ≤ LogP ≤ 5 -2.37
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 190.2
  • LogP ≤ 5 -2.37
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 4
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 145.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
[H]/N=C(/N)\NCC[C@H]([C@@H](C(=O)O)N)O
InChI 
InChI=1S/C6H14N4O3/c7-4(5(12)13)3(11)1-2-10-6(8)9/h3-4,11H,1-2,7H2,(H,12,13)(H4,8,9,10)/t3-,4+/m1/s1
InChIKey 
VIDUVSPOWYVZIC-DMTCNVIQSA-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
PF00252

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_3765.

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)