Ligand profile

PDE

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

Bound to: A0A075B6I6

Via homolog PDB 1kn4 UniProt Q58EU8 Formula C₁₃H₁₇N₂O₈P
Mol. weight 360.26 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
PDE
PDB
1kn4
UniProt (similar protein)
Q58EU8
Target protein
A0A075B6I6

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 360.26 Da
LogP (Crippen) 1.53
H-bond donors 3
H-bond acceptors 6
TPSA 156.07 Ų
Rotatable bonds 9
Aromatic rings 1 / 1
Heavy atoms 24
Fraction sp³ C 0.38
Formula C₁₃H₁₇N₂O₈P

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 156.1
  • −1 ≤ LogP ≤ 5 1.53
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 360.3
  • LogP ≤ 5 1.53
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 6
Veber's rules Fail
  • Rotatable bonds ≤ 10 9
  • TPSA ≤ 140 Ų 156.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
C[C@@H](C(=O)O)NC(=O)CCC[P@@](=O)(O)Oc1ccc(cc1)[N+](=O)[O-]
InChI 
InChI=1S/C13H17N2O8P/c1-9(13(17)18)14-12(16)3-2-8-24(21,22)23-11-6-4-10(5-7-11)15(19)20/h4-7,9H,2-3,8H2,1H3,(H,14,16)(H,17,18)(H,21,22)/t9-/m0/s1
InChIKey 
KBXXIYHMPQZHCH-VIFPVBQESA-N

Provenance

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

Method
LigQ domain
Source
PDB
Binding sites
PF07686

External resources

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

Other ligands for this protein

Quick navigation to other ligands bound to A0A075B6I6.

PDB 54

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

Ligand PDB entry

ChEMBL 29

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)