Ligand profile

ZINC257407589

Virtual-screening candidate from ZINC.

Bound to: VK055_3758 — ribosomal protein L2

Via homolog UniProt P0CX45 Formula C₂₀H₄₁N₅O₇
Tanimoto 0.83
Mol. weight 463.58 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC257407589
UniProt (similar protein)
P0CX45
Tanimoto
0.833
Target protein
VK055_3758

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 463.58 Da
LogP (Crippen) -3.72
H-bond donors 8
H-bond acceptors 12
TPSA 199.73 Ų
Rotatable bonds 7
Aromatic rings 0 / 3
Heavy atoms 32
Fraction sp³ C 1.00
Formula C₂₀H₄₁N₅O₇

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 199.7
  • −1 ≤ LogP ≤ 5 -3.72
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 463.6
  • LogP ≤ 5 -3.72
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 12
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 199.7
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CNC[C@@H]1CC[C@H](N)[C@H](O[C@H]2[C@H](O)[C@@H](O[C@@H]3OC[C@](C)(O)[C@H](NC)[C@@H]3O)[C@@H](N)C[C@H]2N)O1
InChI 
InChI=1S/C20H41N5O7/c1-20(28)8-29-19(14(27)17(20)25-3)32-16-12(23)6-11(22)15(13(16)26)31-18-10(21)5-4-9(30-18)7-24-2/h9-19,24-28H,4-8,21-23H2,1-3H3/t9-,10-,11+,12-,13-,14-,15+,16-,17+,18-,19-,20-/m0/s1
InChIKey 
DNYGXMICFMACRA-ZGVATAJXSA-N

Provenance

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

Method
LigQ nearest_k
Query
LLL
Homolog
P0CX45

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_3758.

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)