Ligand profile

RI2

Ligand co-crystallized with a similar protein (Protein Data Bank).

Bound to: KP13_03382 — Methylthioribose-1-phosphate isomerase

Via homolog PDB 5yfs UniProt O57947 Formula C₅H₁₂O₁₁P₂
Mol. weight 310.09 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RI2
PDB
5yfs
UniProt (similar protein)
O57947
Target protein
KP13_03382

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 310.09 Da
LogP (Crippen) -2.35
H-bond donors 6
H-bond acceptors 7
TPSA 183.21 Ų
Rotatable bonds 5
Aromatic rings 0 / 1
Heavy atoms 18
Fraction sp³ C 1.00
Formula C₅H₁₂O₁₁P₂

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 183.2
  • −1 ≤ LogP ≤ 5 -2.35
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 310.1
  • LogP ≤ 5 -2.35
  • H-bond donors ≤ 5 6
  • H-bond acceptors ≤ 10 7
Veber's rules Fail
  • Rotatable bonds ≤ 10 5
  • TPSA ≤ 140 Ų 183.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C([C@@H]1[C@H]([C@H]([C@H](O1)OP(=O)(O)O)O)O)OP(=O)(O)O
InChI 
InChI=1S/C5H12O11P2/c6-3-2(1-14-17(8,9)10)15-5(4(3)7)16-18(11,12)13/h2-7H,1H2,(H2,8,9,10)(H2,11,12,13)/t2-,3-,4-,5-/m1/s1
InChIKey 
AAAFZMYJJHWUPN-TXICZTDVSA-N

Provenance

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

Method
LigQ nearest_k
Source
PDB
Binding sites
PF01008

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_03382.

PDB 4

Ligands co-crystallized with this protein (structural evidence).

Ligand PDB entry

ZINC 50

Virtual screening candidates selected by structural similarity to known actives (Tanimoto ≥ 0.5).

Compound Similarity (Tanimoto)