Binder profile

ZINC13556870

Virtual-screening candidate from ZINC.

Bound to: PA2840 — ATP-dependent RNA helicase

Via homolog UniProt Q9BUQ8 C6H15O15P3
Tanimoto 0.72
Mol. weight 420.09 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC13556870
UniProt (similar protein)
Q9BUQ8
Tanimoto
0.722
Target protein
PA2840

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 420.09 Da
LogP (Crippen) -3.48
H-bond donors 9
H-bond acceptors 9
TPSA 260.97 Ų
Rotatable bonds 6
Aromatic rings 0 / 1
Heavy atoms 24
Fraction sp³ C 1.00
Formula C6H15O15P3

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 1 violation
  • MW ≤ 500 Da 420.1
  • LogP ≤ 5 -3.48
  • H-bond donors ≤ 5 9
  • H-bond acceptors ≤ 10 9
Veber's rules Fail
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 261.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=P(O)(O)O[C@H]1[C@@H](O)[C@@H](O)[C@H](O)[C@@H](OP(=O)(O)O)[C@@H]1OP(=O)(O)O
InChI 
InChI=1S/C6H15O15P3/c7-1-2(8)4(19-22(10,11)12)6(21-24(16,17)18)5(3(1)9)20-23(13,14)15/h1-9H,(H2,10,11,12)(H2,13,14,15)(H2,16,17,18)/t1-,2-,3-,4+,5-,6-/m0/s1
InChIKey 
GKDKOMAJZATYAY-CNWJWELYSA-N

Provenance

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

Method
LigQ nearest_k
Query
IHP
Homolog
Q9BUQ8

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA2840.

PDB 8

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)