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Protein Structures and Oligomeric States

Enter a protein name, UniProt accession or PDB ID. Name searches ask you to confirm the protein identity before related structures are queried.

Current Protein Identity：P48147 New Search
16PDB entries
49Biological assembly
49chain/assembly records
Main Difference Dimensions in This Set
Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics

Difference tags compare only the current result set; every original PDB and assembly record remains separate.

Related-Structure Differences

Each row represents one biological assembly in one PDB entry; multiple monomers of the same protein are listed separately.

PDB Entry Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Experimental Method Experimental Conditions Structure Quality
3DDU Prolyl Oligopeptidase with GSK552 Deposited 2008-06-06 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 2–710（709 aa）
Not recorded ACT ACETATE ION × 5 552 (6S)-1-chloro-3-[(4-fluorobenzyl)oxy]-6-(pyrrolidin-1-ylcarbonyl)pyrrolo[1,2-a]pyrazin-4(6H)-one × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；pH 4.6；277 K；0 .2M NaoAc 4.6, 9% Peg 4000, VAPOR DIFFUSION, temperature 277K
Resolution 1.56 Å R-free 0.172
9Q5G Human prolyl endopeptidase (PREP) - apo form Deposited 2025-08-20 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded GOL GLYCEROL × 4 SCN THIOCYANATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.63 Å R-free 0.200
9Q5G Human prolyl endopeptidase (PREP) - apo form Deposited 2025-08-20 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded GOL GLYCEROL × 5 SCN THIOCYANATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 3 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.63 Å R-free 0.200
9Q5G Human prolyl endopeptidase (PREP) - apo form Deposited 2025-08-20 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded SCN THIOCYANATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.63 Å R-free 0.200
9Q5X Human prolyl endopeptidase (PREP) - complex with KT-2-74 Deposited 2025-08-21 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded A1CQT 4-chloro-1,3-dimethyl-N-(2-{[3-oxo-3-(pyrrolidin-1-yl)propyl](3-phenylpropyl)amino}ethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 3 SCN THIOCYANATE ION × 1 GOL GLYCEROL × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.41 Å R-free 0.192
9Q5X Human prolyl endopeptidase (PREP) - complex with KT-2-74 Deposited 2025-08-21 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded A1CQT 4-chloro-1,3-dimethyl-N-(2-{[3-oxo-3-(pyrrolidin-1-yl)propyl](3-phenylpropyl)amino}ethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 2 SCN THIOCYANATE ION × 3 GOL GLYCEROL × 6 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.41 Å R-free 0.192
9Q5X Human prolyl endopeptidase (PREP) - complex with KT-2-74 Deposited 2025-08-21 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded A1CQT 4-chloro-1,3-dimethyl-N-(2-{[3-oxo-3-(pyrrolidin-1-yl)propyl](3-phenylpropyl)amino}ethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 PEG DI(HYDROXYETHYL)ETHER × 3 SCN THIOCYANATE ION × 4 GOL GLYCEROL × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.41 Å R-free 0.192
9Q5Y Human prolyl endopeptidase (PREP) - complex with YX45 Deposited 2025-08-21 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 A1CQR 2-[4-chloro-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-1-(pyrrolidin-1-yl)ethan-1-one × 1 GOL GLYCEROL × 5 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.49 Å R-free 0.206
9Q5Y Human prolyl endopeptidase (PREP) - complex with YX45 Deposited 2025-08-21 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded A1CQR 2-[4-chloro-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-1-(pyrrolidin-1-yl)ethan-1-one × 1 GOL GLYCEROL × 9 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.49 Å R-free 0.206
9Q5Y Human prolyl endopeptidase (PREP) - complex with YX45 Deposited 2025-08-21 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded A1CQR 2-[4-chloro-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridin-3-yl]-1-(pyrrolidin-1-yl)ethan-1-one × 1 GOL GLYCEROL × 6 PEG DI(HYDROXYETHYL)ETHER × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.49 Å R-free 0.206
9Q5Z Human prolyl endopeptidase (PREP) - complex with KT-1-147 Deposited 2025-08-21 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded GOL GLYCEROL × 8 PEG DI(HYDROXYETHYL)ETHER × 2 A1CQS 3-methyl-1-(2-phenylethyl)-N-[(pyridin-3-yl)methyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 SCN THIOCYANATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.41 Å R-free 0.187
9Q5Z Human prolyl endopeptidase (PREP) - complex with KT-1-147 Deposited 2025-08-21 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded GOL GLYCEROL × 7 PEG DI(HYDROXYETHYL)ETHER × 1 A1CQS 3-methyl-1-(2-phenylethyl)-N-[(pyridin-3-yl)methyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 SCN THIOCYANATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.41 Å R-free 0.187
9Q5Z Human prolyl endopeptidase (PREP) - complex with KT-1-147 Deposited 2025-08-21 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded GOL GLYCEROL × 4 A1CQS 3-methyl-1-(2-phenylethyl)-N-[(pyridin-3-yl)methyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 SCN THIOCYANATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.41 Å R-free 0.187
9Q62 Human prolyl endopeptidase (PREP) - complex with KT-2-108 Deposited 2025-08-21 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded K POTASSIUM ION × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 A1CQQ 4-chloro-3-methyl-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 SCN THIOCYANATE ION × 8 GOL GLYCEROL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.83 Å R-free 0.239
9Q62 Human prolyl endopeptidase (PREP) - complex with KT-2-108 Deposited 2025-08-21 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded K POTASSIUM ION × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 A1CQQ 4-chloro-3-methyl-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 SCN THIOCYANATE ION × 6 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.83 Å R-free 0.239
9Q62 Human prolyl endopeptidase (PREP) - complex with KT-2-108 Deposited 2025-08-21 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded K POTASSIUM ION × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 A1CQQ 4-chloro-3-methyl-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 SCN THIOCYANATE ION × 1 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.83 Å R-free 0.239
9Q64 Human prolyl endopeptidase (PREP) - complex with KT-2-59 Deposited 2025-08-21 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded A1CQV 1,3-dimethyl-N-[(pyridin-3-yl)methyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 3 SCN THIOCYANATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.94 Å R-free 0.233
9Q64 Human prolyl endopeptidase (PREP) - complex with KT-2-59 Deposited 2025-08-21 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded A1CQV 1,3-dimethyl-N-[(pyridin-3-yl)methyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 7 SCN THIOCYANATE ION × 2 PEG DI(HYDROXYETHYL)ETHER × 2 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.94 Å R-free 0.233
9Q64 Human prolyl endopeptidase (PREP) - complex with KT-2-59 Deposited 2025-08-21 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded A1CQV 1,3-dimethyl-N-[(pyridin-3-yl)methyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.94 Å R-free 0.233
9Q65 Human prolyl endopeptidase (PREP) - complex with KT-2-75 Deposited 2025-08-21 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded A1CQU 4-chloro-1,3-dimethyl-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 5 SCN THIOCYANATE ION × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.89 Å R-free 0.295
9Q65 Human prolyl endopeptidase (PREP) - complex with KT-2-75 Deposited 2025-08-21 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 1–710（710 aa）
Not recorded A1CQU 4-chloro-1,3-dimethyl-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 3 SCN THIOCYANATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.89 Å R-free 0.295
9Q65 Human prolyl endopeptidase (PREP) - complex with KT-2-75 Deposited 2025-08-21 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain F 1–710（710 aa）
Not recorded A1CQU 4-chloro-1,3-dimethyl-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 SCN THIOCYANATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.89 Å R-free 0.295
9Q66 Human prolyl endopeptidase (PREP) - complex with JP-4-1-7 Deposited 2025-08-21 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded A1CQP 4-chloro-1-(cyclohexylmethyl)-3-methyl-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 2 SCN THIOCYANATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 2.01 Å R-free 0.266
9Q66 Human prolyl endopeptidase (PREP) - complex with JP-4-1-7 Deposited 2025-08-21 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded A1CQP 4-chloro-1-(cyclohexylmethyl)-3-methyl-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 2 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 2.01 Å R-free 0.266
9Q66 Human prolyl endopeptidase (PREP) - complex with JP-4-1-7 Deposited 2025-08-21 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded A1CQP 4-chloro-1-(cyclohexylmethyl)-3-methyl-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 1 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 2.01 Å R-free 0.266
9Q6J Human prolyl endopeptidase (PREP) - complex with KT-2-126 Deposited 2025-08-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 A1CQ0 4-chloro-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-3-phenyl-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 8 PEG DI(HYDROXYETHYL)ETHER × 2 SCN THIOCYANATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.75 Å R-free 0.226
9Q6J Human prolyl endopeptidase (PREP) - complex with KT-2-126 Deposited 2025-08-22 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 A1CQ0 4-chloro-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-3-phenyl-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 2 SCN THIOCYANATE ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.75 Å R-free 0.226
9Q6J Human prolyl endopeptidase (PREP) - complex with KT-2-126 Deposited 2025-08-22 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 A1CQ0 4-chloro-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-3-phenyl-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 6 SCN THIOCYANATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.75 Å R-free 0.226
9Q6K Human prolyl endopeptidase (PREP) - complex with JP-2-1-7 Deposited 2025-08-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded A1CQZ 4-chloro-3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 GOL GLYCEROL × 5 PEG DI(HYDROXYETHYL)ETHER × 1 SCN THIOCYANATE ION × 9 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.85 Å R-free 0.272
9Q6K Human prolyl endopeptidase (PREP) - complex with JP-2-1-7 Deposited 2025-08-22 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded A1CQZ 4-chloro-3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 4 SCN THIOCYANATE ION × 8 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.85 Å R-free 0.272
9Q6K Human prolyl endopeptidase (PREP) - complex with JP-2-1-7 Deposited 2025-08-22 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded A1CQZ 4-chloro-3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 GOL GLYCEROL × 3 SCN THIOCYANATE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.85 Å R-free 0.272
9Q6L Human prolyl endopeptidase (PREP) - complex with KT-2-197 Deposited 2025-08-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded SCN THIOCYANATE ION × 9 PEG DI(HYDROXYETHYL)ETHER × 6 GOL GLYCEROL × 12 DMS DIMETHYL SULFOXIDE × 3 A1CQY 3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1-[2-(pyridin-4-yl)ethyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.66 Å R-free 0.216
9Q6L Human prolyl endopeptidase (PREP) - complex with KT-2-197 Deposited 2025-08-22 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded SCN THIOCYANATE ION × 5 PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 9 DMS DIMETHYL SULFOXIDE × 1 A1CQY 3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1-[2-(pyridin-4-yl)ethyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.66 Å R-free 0.216
9Q6L Human prolyl endopeptidase (PREP) - complex with KT-2-197 Deposited 2025-08-22 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded SCN THIOCYANATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 5 DMS DIMETHYL SULFOXIDE × 1 A1CQY 3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1-[2-(pyridin-4-yl)ethyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.66 Å R-free 0.216
9Q6X Human prolyl endopeptidase (PREP) - complex with KT-2-186 Deposited 2025-08-22 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded SCN THIOCYANATE ION × 10 PEG DI(HYDROXYETHYL)ETHER × 6 GOL GLYCEROL × 14 DMS DIMETHYL SULFOXIDE × 3 A1CQ1 4-chloro-3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1-[2-(pyridin-3-yl)ethyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.66 Å R-free 0.214
9Q6X Human prolyl endopeptidase (PREP) - complex with KT-2-186 Deposited 2025-08-22 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded SCN THIOCYANATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 9 DMS DIMETHYL SULFOXIDE × 1 A1CQ1 4-chloro-3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1-[2-(pyridin-3-yl)ethyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.66 Å R-free 0.214
9Q6X Human prolyl endopeptidase (PREP) - complex with KT-2-186 Deposited 2025-08-22 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded SCN THIOCYANATE ION × 3 PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 4 DMS DIMETHYL SULFOXIDE × 1 A1CQ1 4-chloro-3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1-[2-(pyridin-3-yl)ethyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.66 Å R-free 0.214
9XYK Human prolyl endopeptidase (PREP) - complex with JP-7-1-7 Deposited 2025-08-26 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded SCN THIOCYANATE ION × 9 PEG DI(HYDROXYETHYL)ETHER × 6 GOL GLYCEROL × 12 DMS DIMETHYL SULFOXIDE × 3 A1CRL 4-chloro-1-(2-cyclohexylethyl)-3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.73 Å R-free 0.255
9XYK Human prolyl endopeptidase (PREP) - complex with JP-7-1-7 Deposited 2025-08-26 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded SCN THIOCYANATE ION × 5 PEG DI(HYDROXYETHYL)ETHER × 2 GOL GLYCEROL × 8 DMS DIMETHYL SULFOXIDE × 1 A1CRL 4-chloro-1-(2-cyclohexylethyl)-3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.73 Å R-free 0.255
9XYK Human prolyl endopeptidase (PREP) - complex with JP-7-1-7 Deposited 2025-08-26 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded SCN THIOCYANATE ION × 4 PEG DI(HYDROXYETHYL)ETHER × 1 GOL GLYCEROL × 5 DMS DIMETHYL SULFOXIDE × 1 A1CRL 4-chloro-1-(2-cyclohexylethyl)-3-methyl-N-[2-oxo-2-(pyrrolidin-1-yl)ethyl]-1H-pyrazolo[3,4-b]pyridine-5-carboxamide × 1 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.73 Å R-free 0.255
9XYL Human prolyl endopeptidase (PREP) - complex with S17092 Deposited 2025-08-26 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded A1CRK {(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 GOL GLYCEROL × 4 SCN THIOCYANATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.81 Å R-free 0.249
9XYL Human prolyl endopeptidase (PREP) - complex with S17092 Deposited 2025-08-26 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded A1CRK {(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 GOL GLYCEROL × 3 SCN THIOCYANATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.81 Å R-free 0.249
9XYL Human prolyl endopeptidase (PREP) - complex with S17092 Deposited 2025-08-26 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded A1CRK {(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 GOL GLYCEROL × 2 SCN THIOCYANATE ION × 2 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.81 Å R-free 0.249
9XYL Human prolyl endopeptidase (PREP) - complex with S17092 Deposited 2025-08-26 Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain D 1–710（710 aa）
Not recorded A1CRK {(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 GOL GLYCEROL × 1 SCN THIOCYANATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.81 Å R-free 0.249
9XYL Human prolyl endopeptidase (PREP) - complex with S17092 Deposited 2025-08-26 Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain E 1–710（710 aa）
Not recorded A1CRK {(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 GOL GLYCEROL × 2 SCN THIOCYANATE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.81 Å R-free 0.249
9XYL Human prolyl endopeptidase (PREP) - complex with S17092 Deposited 2025-08-26 Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain F 1–710（710 aa）
Not recorded A1CRK {(2S,3aS,7aS)-1-[(1R,2R)-2-phenylcyclopropane-1-carbonyl]octahydro-1H-indol-2-yl}(1,3-thiazolidin-3-yl)methanone × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.81 Å R-free 0.249
9XZZ Human prolyl endopeptidase (PREP) - complex with KYP2047 Deposited 2025-08-28 Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain A 1–710（710 aa）
Not recorded 2P6 (2S)-1-[1-(4-phenylbutanoyl)-L-prolyl]pyrrolidine-2-carbonitrile × 1 GOL GLYCEROL × 7 SCN THIOCYANATE ION × 2 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；in 25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.58 Å R-free 0.200
9XZZ Human prolyl endopeptidase (PREP) - complex with KYP2047 Deposited 2025-08-28 Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain B 1–710（710 aa）
Not recorded 2P6 (2S)-1-[1-(4-phenylbutanoyl)-L-prolyl]pyrrolidine-2-carbonitrile × 1 GOL GLYCEROL × 5 SCN THIOCYANATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；in 25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.58 Å R-free 0.200
9XZZ Human prolyl endopeptidase (PREP) - complex with KYP2047 Deposited 2025-08-28 Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric（1） Consistent with protein count
Chain C 1–710（710 aa）
Not recorded 2P6 (2S)-1-[1-(4-phenylbutanoyl)-L-prolyl]pyrrolidine-2-carbonitrile × 1 GOL GLYCEROL × 3 SCN THIOCYANATE ION × 3 B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；in 25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5
Resolution 1.58 Å R-free 0.200

This page presents structural evidence recorded in PDB/mmCIF.“No recorded non-water small molecule” does not prove that the experimental sample was ligand-free; experimental conditions belong to the PDB experiment, while ligands and copy counts are shown for each biological assembly.