Ligand profile

ZINC5201841

Virtual-screening candidate from ZINC.

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

Via homolog UniProt A1WJM2 Formula C₁₂H₂₇NO₁₀
Tanimoto 0.65
Mol. weight 345.35 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
ZINC5201841
UniProt (similar protein)
A1WJM2
Tanimoto
0.647
Target protein
KP13_00005

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 345.35 Da
LogP (Crippen) -6.55
H-bond donors 11
H-bond acceptors 11
TPSA 214.33 Ų
Rotatable bonds 12
Aromatic rings 0 / 0
Heavy atoms 23
Fraction sp³ C 1.00
Formula C₁₂H₂₇NO₁₀

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 214.3
  • −1 ≤ LogP ≤ 5 -6.55
Lipinski's Rule of Five Fail 2 violations
  • MW ≤ 500 Da 345.3
  • LogP ≤ 5 -6.55
  • H-bond donors ≤ 5 11
  • H-bond acceptors ≤ 10 11
Veber's rules Fail
  • Rotatable bonds ≤ 10 12
  • TPSA ≤ 140 Ų 214.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
OC[C@@H](O)[C@@H](O)[C@@H](O)[C@@H](O)CNC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO
InChI 
InChI=1S/C12H27NO10/c14-3-7(18)11(22)9(20)5(16)1-13-2-6(17)10(21)12(23)8(19)4-15/h5-23H,1-4H2/t5-,6+,7-,8-,9-,10+,11-,12-/m1/s1
InChIKey 
KXONZRPGKNOGCG-VIXLETMSSA-N

Provenance

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

Method
LigQ nearest_k
Query
TLZ
Homolog
A1WJM2

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)