Ligand profile

ZINC199362416

Virtual-screening candidate from ZINC.

Bound to: VK055_3755 — 50S ribosomal protein L3

Via homolog UniProt P60438 Formula C₂₂H₂₄N₂O₈
Tanimoto 0.69
Mol. weight 444.44 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC199362416
UniProt (similar protein)
P60438
Tanimoto
0.688
Target protein
VK055_3755

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 444.44 Da
LogP (Crippen) -0.37
H-bond donors 6
H-bond acceptors 9
TPSA 181.62 Ų
Rotatable bonds 2
Aromatic rings 1 / 4
Heavy atoms 32
Fraction sp³ C 0.41
Formula C₂₂H₂₄N₂O₈

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 181.6
  • −1 ≤ LogP ≤ 5 -0.37
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 444.4
  • LogP ≤ 5 -0.37
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 181.6
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CN(C)[C@@H]1C(=O)C(C(N)=O)=C(O)[C@]2(O)C(=O)C3=C(O)c4c(O)cccc4[C@](C)(O)[C@@H]3C[C@@H]12
InChI 
InChI=1S/C22H24N2O8/c1-21(31)8-5-4-6-11(25)12(8)16(26)13-9(21)7-10-15(24(2)3)17(27)14(20(23)30)19(29)22(10,32)18(13)28/h4-6,9-10,15,25-26,29,31-32H,7H2,1-3H3,(H2,23,30)/t9-,10+,15+,21+,22-/m1/s1
InChIKey 
NWXMGUDVXFXRIG-INTQRVTCSA-N

Provenance

Annotation context from LigQ_2, the internal Target step that collects PDB, ChEMBL, and ZINC ligand evidence.

Method
LigQ sequence
Query
TAC
Homolog
P60438

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_3755.

PDB 6

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 49

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)