Binder profile

ZINC4545928

Virtual-screening candidate from ZINC.

Bound to: PA4670 — ribose-phosphate pyrophosphokinase

Via homolog UniProt Q58761 C6H13O9P
Tanimoto 0.89
Mol. weight 260.13 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC4545928
UniProt (similar protein)
Q58761
Tanimoto
0.889
Target protein
PA4670

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 260.13 Da
LogP (Crippen) -3.26
H-bond donors 6
H-bond acceptors 7
TPSA 164.75 Ų
Rotatable bonds 7
Aromatic rings 0 / 0
Heavy atoms 16
Fraction sp³ C 0.83
Formula C6H13O9P

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 260.1
  • LogP ≤ 5 -3.26
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 7
  • TPSA ≤ 140 Ų 164.8
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O=C[C@@H](O)[C@@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O
InChI 
InChI=1S/C6H13O9P/c7-1-3(8)5(10)6(11)4(9)2-15-16(12,13)14/h1,3-6,8-11H,2H2,(H2,12,13,14)/t3-,4-,5-,6+/m1/s1
InChIKey 
VFRROHXSMXFLSN-KAZBKCHUSA-N

Provenance

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

Method
LigQ nearest_k
Query
R5P
Homolog
Q58761

External resources

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

Other binders for this protein

Quick navigation to other ligands bound to PA4670.

PDB 2

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)