Binder profile

ZINC258828116

Virtual-screening candidate from ZINC.

Bound to: PA0933 — 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD

Via homolog UniProt Q97R12 C21H40O10
Tanimoto 0.58
Mol. weight 452.54 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC258828116
UniProt (similar protein)
Q97R12
Tanimoto
0.579
Target protein
PA0933

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 452.54 Da
LogP (Crippen) -0.24
H-bond donors 1
H-bond acceptors 10
TPSA 103.30 Ų
Rotatable bonds 27
Aromatic rings 0 / 0
Heavy atoms 31
Fraction sp³ C 0.90
Formula C21H40O10

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.

Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 452.5
  • LogP ≤ 5 -0.24
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 10
Veber's rules Fail
  • Rotatable bonds ≤ 10 27
  • TPSA ≤ 140 Ų 103.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C#CCOCCOCCOCCOCCOCCOCCOCCOCCOCCO
InChI 
InChI=1S/C21H40O10/c1-2-4-23-6-8-25-10-12-27-14-16-29-18-20-31-21-19-30-17-15-28-13-11-26-9-7-24-5-3-22/h1,22H,3-21H2
InChIKey 
FBQGPFAGZKPHQT-UHFFFAOYSA-N

Provenance

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

Method
LigQ nearest_k
Query
P6G
Homolog
Q97R12

External resources

Open this ligand in third-party databases and cheminformatics tools.

Other binders for this protein

Quick navigation to other ligands bound to PA0933.

ZINC 49

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

Compound Similarity (Tanimoto)