3ddu

Prolyl Oligopeptidase with GSK552

Method: X-RAY DIFFRACTION D_max: 81.2 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Prolyl endopeptidase

Homo sapiens

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 2–710	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

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 3DDU	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9Q5G Human prolyl endopeptidase (PREP) - apo form Deposited 2025-08-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	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

15 other PDB entries and 48 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PPCE_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–709； UniProt 2–710

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	3ddu
Deposition date deposition_date	2008-06-06
Structure title title	Prolyl Oligopeptidase with GSK552
Keywords keywords	POP, Prolyl Oligopeptidase, endopeptidase, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	26.86 Å
Radius of gyration Rg (electron density) rg_electron	25.74 Å
Forward intensity I(0) i0	101480000.00
Molecular weight molecular_weight	80383.0 kDa
Excluded volume excluded_volume	100930 Å³
Envelope volume envelope_volume	121090 Å³
Hydration-shell volume shell_volume	37847 Å³
Envelope diameter envelope_diameter	84.4 Å
Shell Rg shell_rg	34.50 Å
Envelope Rg envelope_rg	25.57 Å
Shape Rg shape_rg	25.72 Å
Total Rg total_rg	26.70 Å
Total atoms total_atoms	5677
Residues n_residues	707
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	81.2 Å
Rg (real space) rg_real	26.68 Å
Rg uncertainty (real space) rg_real_error	0.42 Å
I(0) (real space) i0_real	1.0150e+08
I(0) uncertainty (real space) i0_real_error	1.3030e+06
Rg (reciprocal space) rg_reciprocal	26.73 Å
I(0) (reciprocal space) i0_reciprocal	101500000.0000
Solution quality estimate total_estimate	0.9017
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.4 Å
Skewness Skewness skewness	0.148
Kurtosis Kurtosis kurtosis	-0.429
Angular range angular_range	— – 0.2950 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	18110000.0000
Real-space data points n_real_points	60
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.928; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.949

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Prolyl endopeptidase
Molecular weight formula_weight	80678.1 kDa
EC 编号 ec_number	3.4.21.26
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	6931

LSFQYPDVYRDETAVQDYHGHKICDPYAWLEDPDSEQTKAFVEAQNKITVPFLEQCPIRGLYKERMTELYDYPKYSCHFKKGKRYFYFYNTGLQNQRVLYVQDSLEGEARVFLDPNILSDDGTVALRGYAFSEDGEYFAYGLSASGSDWVTIKFMKVDGAKELPDVLERVKFSCMAWTHDGKGMFYNSYPQQDGKSDGTETSTNLHQKLYYHVLGTDQSEDILCAEFPDEPKWMGGAELSDDGRYVLLSIREGCDPVNRLWYCDLQQESSGIAGILKWVKLIDNFEGEYDYVTNEGTVFTFKTNRHSPNYRVINIDFTDPEESKWKVLVPEHEKDVLEWIACVRSNFLVLCYLHDVKNTLQLHDLTTGALLKIFPLDVGSIVGYSGQKKDTEIFYQFTSFLSPGIIYHCDLTKEELEPRVFREVTVKGIDASDYQTVQIFYPSKDGTKIPMFIVHKKGIKLDGSHPAFLYGYGGFNISITPNYSVSRLIFVRHMGGILAVANIRGGGEYGETWHKGGILANKQNCFDDFQCAAEYLIKEGYTSPKRLTINGGSNGGLLVAACANQRPDLFGCVIAQVGVMDMLKFHKYTIGHAWTTDYGCSDSKQHFEWLVKYSPLHNVKLPEADDIQYPSMLLLTADHDDRVVPLHSLKFIATLQYIVGRSRKQNNPLLIHVDTKAGHGAGKPTAKVIEEVSDMFAFIARCLNVDWIP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 3 Entity 3 non-polymer

Description description	(6S)-1-chloro-3-[(4-fluorobenzyl)oxy]-6-(pyrrolidin-1-ylcarbonyl)pyrrolo[1,2-a]pyrazin-4(6H)-one
Molecular weight formula_weight	389.8 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1234

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ddua1
Class class	b — All beta proteins
Fold Fold fold	b.69 — 7-bladed beta-propeller
Superfamily Superfamily superfamily	b.69.7 — Peptidase/esterase 'gauge' domain
Family Family family	b.69.7.1 — Prolyl oligopeptidase, N-terminal domain

Domain ID domain_id	d3ddua2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.69 — alpha/beta-Hydrolases
Superfamily Superfamily superfamily	c.69.1 — alpha/beta-Hydrolases
Family Family family	c.69.1.4 — Prolyl oligopeptidase, C-terminal domain

CATH v4.4 (2 domains)

Domain ID domain_id	3dduA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1820 — Alpha/Beta hydrolase fold, catalytic domain

Domain ID domain_id	3dduA02
Class class	2 — Mainly Beta
Architecture architecture	130 — 7 Propeller
Topology topology	10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily	120 — Prolyl oligopeptidase, N-terminal domain

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8. Citations (1)

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Unit-cell length a length_a	71.221 Å
Unit-cell length b length_b	99.883 Å
Unit-cell length c length_c	111.853 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.560 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	0.1490
R_work r_work	0.1470
R_free r_free	0.1720

fit	/app/data/saxs_computation/dd/3ddu/3ddu.fit
pddf	/app/data/pr_computation/dd/3ddu/3ddu.pr.out
profile	/app/data/saxs_computation/dd/3ddu/3ddu.dat