Binder profile

ZINC115086873

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q97R12 C8H19NO5
Tanimoto 0.69
Mol. weight 209.24 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC115086873
UniProt (similar protein)
Q97R12
Tanimoto
0.688
Target protein
PA0933

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 209.24 Da
LogP (Crippen) -1.08
H-bond donors 2
H-bond acceptors 6
TPSA 83.17 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 1.00
Formula C8H19NO5

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 209.2
  • LogP ≤ 5 -1.08
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 83.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
NOCCOCCOCCOCCO
InChI 
InChI=1S/C8H19NO5/c9-14-8-7-13-6-5-12-4-3-11-2-1-10/h10H,1-9H2
InChIKey 
CMZGGYJEHLUUIG-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)