Binder profile

ZINC96503425

Virtual-screening candidate from ZINC.

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

Via homolog UniProt Q97R12 C9H18O6
Tanimoto 0.58
Mol. weight 222.24 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC96503425
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 222.24 Da
LogP (Crippen) -0.50
H-bond donors 2
H-bond acceptors 5
TPSA 85.22 Ų
Rotatable bonds 11
Aromatic rings 0 / 0
Heavy atoms 15
Fraction sp³ C 0.89
Formula C9H18O6

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 222.2
  • LogP ≤ 5 -0.50
  • H-bond donors ≤ 5 2
  • H-bond acceptors ≤ 10 5
Veber's rules Fail
  • Rotatable bonds ≤ 10 11
  • TPSA ≤ 140 Ų 85.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C(O)CCOCCOCCOCCO
InChI 
InChI=1S/C9H18O6/c10-2-4-14-6-8-15-7-5-13-3-1-9(11)12/h10H,1-8H2,(H,11,12)
InChIKey 
NJUMHPXJVKDMAW-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)