Binder profile

ZINC1580161

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q97R12 C9H20O5
Tanimoto 0.69
Mol. weight 208.25 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC1580161
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 208.25 Da
LogP (Crippen) -0.33
H-bond donors 1
H-bond acceptors 5
TPSA 57.15 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 14
Fraction sp³ C 1.00
Formula C9H20O5

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 208.3
  • LogP ≤ 5 -0.33
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 57.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
COCCOCCOCCOCCO
InChI 
InChI=1S/C9H20O5/c1-11-4-5-13-8-9-14-7-6-12-3-2-10/h10H,2-9H2,1H3
InChIKey 
ZNYRFEPBTVGZDN-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)