Ligand profile

XPD

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

Bound to: KP13_01723 — Lysophospholipase L2

Via homolog PDB 7l4t UniProt Q99685 Formula C₂₁H₂₀ClFN₂O₄
Mol. weight 418.85 Da
Permeability High
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
XPD
PDB
7l4t
UniProt (similar protein)
Q99685
Target protein
KP13_01723

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 418.85 Da
LogP (Crippen) 3.74
H-bond donors 1
H-bond acceptors 4
TPSA 67.87 Ų
Rotatable bonds 4
Aromatic rings 2 / 4
Heavy atoms 29
Fraction sp³ C 0.33
Formula C₂₁H₂₀ClFN₂O₄

Drug-likeness

Descriptor-based ADME screening flags from SMILES. These are not experimental toxicity results.

Permeability proxy High

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 67.9
  • −1 ≤ LogP ≤ 5 3.74
Lipinski's Rule of Five Pass 0 violations
  • MW ≤ 500 Da 418.9
  • LogP ≤ 5 3.74
  • H-bond donors ≤ 5 1
  • H-bond acceptors ≤ 10 4
Veber's rules Pass
  • Rotatable bonds ≤ 10 4
  • TPSA ≤ 140 Ų 67.9
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
c1cc2c(cc1C(=O)N3CCC(CC3)COc4ccc(cc4Cl)F)NC(=O)CO2
InChI 
InChI=1S/C21H20ClFN2O4/c22-16-10-15(23)2-4-18(16)28-11-13-5-7-25(8-6-13)21(27)14-1-3-19-17(9-14)24-20(26)12-29-19/h1-4,9-10,13H,5-8,11-12H2,(H,24,26)
InChIKey 
UUUUFICXTVCJQV-UHFFFAOYSA-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
PF12146

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_01723.

PDB 6

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)