Ligand profile

RDD

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

Bound to: KP13_00667 — Glycogen phosphorylase

Via homolog PDB 3bd6 UniProt P00489 Formula C₈H₁₁N₃O₇
Mol. weight 261.19 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
RDD
PDB
3bd6
UniProt (similar protein)
P00489
Target protein
KP13_00667

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 261.19 Da
LogP (Crippen) -4.16
H-bond donors 5
H-bond acceptors 8
TPSA 157.64 Ų
Rotatable bonds 2
Aromatic rings 1 / 2
Heavy atoms 18
Fraction sp³ C 0.62
Formula C₈H₁₁N₃O₇

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 157.6
  • −1 ≤ LogP ≤ 5 -4.16
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 261.2
  • LogP ≤ 5 -4.16
  • H-bond donors ≤ 5 5
  • H-bond acceptors ≤ 10 8
Veber's rules Fail
  • Rotatable bonds ≤ 10 2
  • TPSA ≤ 140 Ų 157.6
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)N2C(=O)NC(=O)NC2=O)O)O)O
InChI 
InChI=1S/C8H11N3O7/c12-1-2-3(13)4(14)5(18-2)11-7(16)9-6(15)10-8(11)17/h2-5,12-14H,1H2,(H2,9,10,15,16,17)/t2-,3-,4-,5-/m1/s1
InChIKey 
DKOBRNXETUUICC-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
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)