Ligand profile

GPP

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

Bound to: KP13_03723 — Cyclopropane-fatty-acyl-phospholipid synthase

Via homolog PDB 4f86 UniProt D3KYU3 Formula C₁₀H₂₀O₇P₂
Mol. weight 314.21 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
GPP
PDB
4f86
UniProt (similar protein)
D3KYU3
Target protein
KP13_03723

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 314.21 Da
LogP (Crippen) 2.91
H-bond donors 3
H-bond acceptors 4
TPSA 113.29 Ų
Rotatable bonds 8
Aromatic rings 0 / 0
Heavy atoms 19
Fraction sp³ C 0.60
Formula C₁₀H₂₀O₇P₂

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 113.3
  • −1 ≤ LogP ≤ 5 2.91
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 314.2
  • LogP ≤ 5 2.91
  • H-bond donors ≤ 5 3
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 8
  • TPSA ≤ 140 Ų 113.3
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(=CCC/C(=C/CO[P@@](=O)(O)OP(=O)(O)O)/C)C
InChI 
InChI=1S/C10H20O7P2/c1-9(2)5-4-6-10(3)7-8-16-19(14,15)17-18(11,12)13/h5,7H,4,6,8H2,1-3H3,(H,14,15)(H2,11,12,13)/b10-7+
InChIKey 
GVVPGTZRZFNKDS-JXMROGBWSA-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
PF02353

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_03723.

PDB 7

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)