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9q5y

Human prolyl endopeptidase (PREP) - complex with YX45

Method: X-RAY DIFFRACTION Dmax: 173.7 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Prolyl endopeptidase

Homo sapiens

UniProt P48147

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 1–710 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
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain B； UniProt 1–710 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
3 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain C； UniProt 1–710 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

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 9Q5Y Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3DDU Prolyl Oligopeptidase with GSK552 Deposited 2008-06-06 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
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 Different ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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
9Q5Z Human prolyl endopeptidase (PREP) - complex with KT-1-147 Deposited 2025-08-21 Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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 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 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 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 46 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 2–711； UniProt 1–710 Author chain B； PDBConstruct 2–711； UniProt 1–710 Author chain C； PDBConstruct 2–711； UniProt 1–710

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

SAXS profile for 9q5y

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9q5y
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9q5y
Deposition date deposition_date2025-08-21
Structure title titleHuman prolyl endopeptidase (PREP) - complex with YX45
Keywords keywordsapo form, peptide cleavage, HYDROLASE, HYDROLASE-HYDROLASE INHIBITOR complex; HYDROLASE/HYDROLASE INHIBITOR
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier53.33 Å
Radius of gyration Rg (electron density) rg_electron54.04 Å
Forward intensity I(0) i0828382000.00
Molecular weight molecular_weight244730.0 kDa
Excluded volume excluded_volume307990 ų
Envelope volume envelope_volume420600 ų
Hydration-shell volume shell_volume71548 ų
Envelope diameter envelope_diameter187.2 Å
Shell Rg shell_rg49.41 Å
Envelope Rg envelope_rg53.15 Å
Shape Rg shape_rg54.05 Å
Total Rg total_rg53.82 Å
Total atoms total_atoms34087
Residues n_residues2121
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax173.7 Å
Rg (real space) rg_real53.89 Å
Rg uncertainty (real space) rg_real_error2.22 Å
I(0) (real space) i0_real8.2840e+08
I(0) uncertainty (real space) i0_real_error1.7210e+07
Rg (reciprocal space) rg_reciprocal52.84 Å
I(0) (reciprocal space) i0_reciprocal827100000.0000
Solution quality estimate total_estimate0.5509
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary46.3 Å
Skewness Skewness skewness0.590
Kurtosis Kurtosis kurtosis-0.447
Angular range angular_range— – 0.1500 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha214700000.0000
Real-space data points n_real_points31
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.700; Stabil: 1.000; Sysdev: 0.062; Positv: 1.000; Valcen: 0.860; Smooth: 0.012
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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8. Citations (1)

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9. Files and Curves (10)