Ligand profile

ZINC255980411

Virtual-screening candidate from ZINC.

Bound to: KP13_00005 — D-ribose-binding periplasmic protein

Via homolog UniProt A6VKT0 Formula C₁₅H₂₆O₁₃
Tanimoto 0.58
Mol. weight 414.36 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC255980411
UniProt (similar protein)
A6VKT0
Tanimoto
0.577
Target protein
KP13_00005

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 414.36 Da
LogP (Crippen) -5.66
H-bond donors 8
H-bond acceptors 13
TPSA 207.99 Ų
Rotatable bonds 4
Aromatic rings 0 / 3
Heavy atoms 28
Fraction sp³ C 1.00
Formula C₁₅H₂₆O₁₃

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.

  • TPSA ≤ 90 Ų 208.0
  • −1 ≤ LogP ≤ 5 -5.66
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 414.4
  • LogP ≤ 5 -5.66
  • H-bond donors ≤ 5 8
  • H-bond acceptors ≤ 10 13
Veber's rules Fail
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 208.0
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
O[C@H]1OC[C@@H](O[C@H]2OC[C@@H](O[C@H]3OC[C@@H](O)[C@@H](O)[C@@H]3O)[C@@H](O)[C@H]2O)[C@@H](O)[C@H]1O
InChI 
InChI=1S/C15H26O13/c16-4-1-25-14(11(21)7(4)17)28-6-3-26-15(12(22)9(6)19)27-5-2-24-13(23)10(20)8(5)18/h4-23H,1-3H2/t4-,5-,6-,7-,8-,9-,10-,11+,12-,13+,14-,15-/m1/s1
InChIKey 
JCSJTDYCNQHPRJ-ZSEPQWBBSA-N

Provenance

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

Method
LigQ nearest_k
Query
RIP
Homolog
A6VKT0

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to KP13_00005.

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)