Ligand profile

78E

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

Bound to: KP13_00717 — Peptidyl-prolyl cis-trans isomerase A

Via homolog PDB 5t9w UniProt P62937 Formula C₃₀H₄₂N₄O₆
Mol. weight 554.69 Da
Permeability Check
PAINS Clean

Identifiers

Database identifiers and provenance.

Ligand ID
78E
PDB
5t9w
UniProt (similar protein)
P62937
Target protein
KP13_00717

Structure

2D representation rendered from SMILES.

Physicochemical properties

Computed with RDKit from SMILES.

Molecular weight 554.69 Da
LogP (Crippen) 2.68
H-bond donors 4
H-bond acceptors 7
TPSA 137.07 Ų
Rotatable bonds 3
Aromatic rings 1 / 3
Heavy atoms 40
Fraction sp³ C 0.53
Formula C₃₀H₄₂N₄O₆

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 137.1
  • −1 ≤ LogP ≤ 5 2.68
Lipinski's Rule of Five Pass 1 violation
  • MW ≤ 500 Da 554.7
  • LogP ≤ 5 2.68
  • H-bond donors ≤ 5 4
  • H-bond acceptors ≤ 10 7
Veber's rules Pass
  • Rotatable bonds ≤ 10 3
  • TPSA ≤ 140 Ų 137.1
PAINS Clean

No PAINS structural alerts detected.

Chemical representations

Canonical representations for cheminformatics workflows.

SMILES 
CC(C)[C@H]1C(=O)N[C@H](C(=O)N2CCC[C@H](N2)C(=O)OCC/C=C/C=C/CCCCC(=O)N1)Cc3cccc(c3)O
InChI 
InChI=1S/C30H42N4O6/c1-21(2)27-28(37)31-25(20-22-13-11-14-23(35)19-22)29(38)34-17-12-15-24(33-34)30(39)40-18-10-8-6-4-3-5-7-9-16-26(36)32-27/h3-4,6,8,11,13-14,19,21,24-25,27,33,35H,5,7,9-10,12,15-18,20H2,1-2H3,(H,31,37)(H,32,36)/b4-3+,8-6+/t24-,25-,27-/m0/s1
InChIKey 
ZXIFDXMZMTULOX-WDJUPVIMSA-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
PF00160

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_00717.

PDB 39

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)