Ligand profile

D1I

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

Bound to: KP13_00667 — Glycogen phosphorylase

Via homolog PDB 4eke UniProt P00489 Formula C₁₇H₂₄N₂O₇
Mol. weight 368.39 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
D1I
PDB
4eke
UniProt (similar protein)
P00489
Target protein
KP13_00667

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 368.39 Da
LogP (Crippen) -0.31
H-bond donors 4
H-bond acceptors 9
TPSA 138.18 Ų
Rotatable bonds 6
Aromatic rings 2 / 3
Heavy atoms 26
Fraction sp³ C 0.65
Formula C₁₇H₂₄N₂O₇

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 138.2
  • −1 ≤ LogP ≤ 5 -0.31
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 368.4
  • LogP ≤ 5 -0.31
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 9
Veber's rules Pass
  • Rotatable bonds ≤ 10 6
  • TPSA ≤ 140 Ų 138.2
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CCCCCC1=CC2=CN(C(=O)N=C2O1)[C@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)O
InChI 
InChI=1S/C17H24N2O7/c1-2-3-4-5-10-6-9-7-19(17(24)18-15(9)25-10)16-14(23)13(22)12(21)11(8-20)26-16/h6-7,11-14,16,20-23H,2-5,8H2,1H3/t11-,12-,13+,14-,16-/m1/s1
InChIKey 
OPBPIQMYHFDOAO-XYFZXANASA-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
PF00343

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_00667.

PDB 115

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

Ligand PDB entry

ChEMBL 100

Compounds with measured inhibitory activity on this target (higher pchembl = more potent).

Compound Potency (pchembl)

ZINC 50

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

Compound Similarity (Tanimoto)