Ligand profile

ZINC4879577

Virtual-screening candidate from ZINC.

Bound to: VK055_3755 — 50S ribosomal protein L3

Via homolog UniProt P60438 Formula C₂₀H₁₉NO₈
Tanimoto 0.69
Mol. weight 401.37 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4879577
UniProt (similar protein)
P60438
Tanimoto
0.689
Target protein
VK055_3755

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 401.37 Da
LogP (Crippen) 0.25
H-bond donors 6
H-bond acceptors 8
TPSA 178.38 Ų
Rotatable bonds 1
Aromatic rings 1 / 4
Heavy atoms 29
Fraction sp³ C 0.35
Formula C₂₀H₁₉NO₈

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 178.4
  • −1 ≤ LogP ≤ 5 0.25
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 401.4
  • LogP ≤ 5 0.25
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 1
  • TPSA ≤ 140 Ų 178.4
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@]1(O)c2cccc(O)c2C(=O)C2=C(O)[C@@]3(O)C(=O)C(C(N)=O)=C(O)C[C@@H]3C[C@@H]21
InChI 
InChI=1S/C20H19NO8/c1-19(28)8-3-2-4-10(22)12(8)15(24)13-9(19)5-7-6-11(23)14(18(21)27)17(26)20(7,29)16(13)25/h2-4,7,9,22-23,25,28-29H,5-6H2,1H3,(H2,21,27)/t7-,9-,19-,20+/m0/s1
InChIKey 
SRPCXEFYFVDUFQ-JPTZLNLOSA-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)