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- PDB-9q6j: Human prolyl endopeptidase (PREP) - complex with KT-2-126 -

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Basic information

Entry
Database: PDB / ID: 9q6j
TitleHuman prolyl endopeptidase (PREP) - complex with KT-2-126
ComponentsProlyl endopeptidase
KeywordsHYDROLASE/HYDROLASE INHIBITOR / inhibitor-bound / peptide cleavage / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


prolyl oligopeptidase / oligopeptidase activity / angiotensin maturation / metallocarboxypeptidase activity / serine-type peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region / nucleus / membrane ...prolyl oligopeptidase / oligopeptidase activity / angiotensin maturation / metallocarboxypeptidase activity / serine-type peptidase activity / serine-type endopeptidase activity / proteolysis / extracellular region / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Peptidase S9A, prolyl oligopeptidase / Peptidase S9A, N-terminal domain / Prolyl oligopeptidase, N-terminal beta-propeller domain / Prolyl endopeptidase family serine active site. / Peptidase S9, serine active site / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Prolyl endopeptidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsFucci, I.J. / Thakur, K. / Pandian, J. / Yoo, E. / Monteiro, D.C.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: J.Med.Chem. / Year: 2026
Title: Structure-Guided Optimization of 4-Chloro-Pyrazolopyridine Analogs for Covalent PREP Inhibition.
Authors: Thakur, K. / Fucci, I. / Pandian, J. / Suazo, K.F. / Monteiro, D.C.F. / Yoo, E.
History
DepositionAug 22, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Prolyl endopeptidase
B: Prolyl endopeptidase
C: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,51439
Polymers242,5543
Non-polymers4,96036
Water33,3821853
1
A: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,04117
Polymers80,8511
Non-polymers2,19016
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,11010
Polymers80,8511
Non-polymers1,2599
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,36312
Polymers80,8511
Non-polymers1,51111
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)106.127, 66.936, 157.183
Angle α, β, γ (deg.)90, 99.284, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Prolyl endopeptidase / PE / Post-proline cleaving enzyme


Mass: 80851.367 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PREP, PEP / Production host: Escherichia coli (E. coli) / References: UniProt: P48147, prolyl oligopeptidase

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Non-polymers , 6 types, 1889 molecules

#2: Chemical
ChemComp-B3P / 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL


Mass: 282.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#3: Chemical ChemComp-A1CQ0 / 4-chloro-N-[3-oxo-3-(pyrrolidin-1-yl)propyl]-3-phenyl-1-(2-phenylethyl)-1H-pyrazolo[3,4-b]pyridine-5-carboxamide


Mass: 502.007 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C28H28ClN5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: CNS
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1853 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 25-30% PEG 3350, 200 mM KSCN and 100 mM bis-tris propane pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.919764 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 5, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919764 Å / Relative weight: 1
ReflectionResolution: 1.75→43.8 Å / Num. obs: 167666 / % possible obs: 94.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 16.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.241 / Rpim(I) all: 0.099 / Rrim(I) all: 0.26 / Net I/σ(I): 6.4
Reflection shellResolution: 1.75→1.93 Å / Rmerge(I) obs: 1.544 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 8383 / CC1/2: 0.64 / Rpim(I) all: 0.647 / Rrim(I) all: 1.677 / % possible all: 57.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0430 (refmacat 0.4.105)refinement
autoPROCdata reduction
autoPROCdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.75→43.8 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.923 / SU B: 8.427 / SU ML: 0.128 / Cross valid method: FREE R-VALUE / ESU R: 0.155 / ESU R Free: 0.153
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2261 8371 4.993 %
Rwork0.1642 159294 -
all0.167 --
obs-167665 76.589 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 23.884 Å2
Baniso -1Baniso -2Baniso -3
1-0.244 Å20 Å2-0.142 Å2
2---0.36 Å2-0 Å2
3---0.154 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17019 0 324 1853 19196
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01217873
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616377
X-RAY DIFFRACTIONr_angle_refined_deg2.4111.8224200
X-RAY DIFFRACTIONr_angle_other_deg0.8041.76137864
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.56652143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.9797.673101
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg8.25153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.228102932
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.33510858
X-RAY DIFFRACTIONr_chiral_restr0.1120.22547
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0220853
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024159
X-RAY DIFFRACTIONr_nbd_refined0.2150.23560
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2050.216101
X-RAY DIFFRACTIONr_nbtor_refined0.1930.28615
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0960.29534
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1910.21617
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1590.29
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2710.237
X-RAY DIFFRACTIONr_nbd_other0.2550.2126
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2680.259
X-RAY DIFFRACTIONr_mcbond_it1.3671.0128521
X-RAY DIFFRACTIONr_mcbond_other1.3441.0118518
X-RAY DIFFRACTIONr_mcangle_it2.0571.80610639
X-RAY DIFFRACTIONr_mcangle_other2.0571.80610640
X-RAY DIFFRACTIONr_scbond_it2.4061.2759352
X-RAY DIFFRACTIONr_scbond_other2.4061.2759353
X-RAY DIFFRACTIONr_scangle_it3.6142.2213549
X-RAY DIFFRACTIONr_scangle_other3.6142.22113550
X-RAY DIFFRACTIONr_lrange_it5.82413.48320818
X-RAY DIFFRACTIONr_lrange_other5.76211.83220364
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.7970.31430.34249X-RAY DIFFRACTION0.3228
1.797-1.8460.359340.316595X-RAY DIFFRACTION4.0135
1.846-1.90.3311830.2853369X-RAY DIFFRACTION23.2415
1.9-1.9580.2944330.2638567X-RAY DIFFRACTION60.8478
1.958-2.0220.2916610.25312584X-RAY DIFFRACTION92.3383
2.022-2.0930.2766690.23113004X-RAY DIFFRACTION98.2609
2.093-2.1720.2646500.21212538X-RAY DIFFRACTION98.4032
2.172-2.260.2446590.1912032X-RAY DIFFRACTION98.4562
2.26-2.360.2386260.17311652X-RAY DIFFRACTION98.6264
2.36-2.4750.2435670.16611195X-RAY DIFFRACTION98.7739
2.475-2.6090.2435660.15810569X-RAY DIFFRACTION98.9074
2.609-2.7660.2275060.15210083X-RAY DIFFRACTION99.083
2.766-2.9570.2214970.1519471X-RAY DIFFRACTION99.0756
2.957-3.1920.2194980.1468859X-RAY DIFFRACTION99.2785
3.192-3.4950.2194140.1428188X-RAY DIFFRACTION99.3532
3.495-3.9050.1973930.1367415X-RAY DIFFRACTION99.4903
3.905-4.5030.1673640.1116564X-RAY DIFFRACTION99.5975
4.503-5.50.1742930.1165593X-RAY DIFFRACTION99.6614
5.5-7.7180.2132180.1564395X-RAY DIFFRACTION99.7405
7.718-43.80.2161370.1662573X-RAY DIFFRACTION99.9263
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.790.2261-0.21250.6909-0.04540.4990.0237-0.04810.02550.02850.0031-0.0667-0.03090.0608-0.02680.0039-0.0086-0.00010.0338-0.0090.0108-1.19720.634553.911
21.1911-0.1384-0.4770.8502-0.04430.9443-0.0361-0.04980.05990.04910.0422-0.03940.07330.024-0.00610.0607-0.0035-0.00460.0778-0.02110.034-26.36533.7913-0.8574
30.82120.0062-0.31520.7027-0.02030.9407-0.0267-0.0947-0.00290.08260.0399-0.15980.12590.2043-0.01320.04060.0479-0.03610.1138-0.02360.0544-51.8722-0.5002-51.0636
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAp4 - 815
2X-RAY DIFFRACTION2ALLBp4 - 808
3X-RAY DIFFRACTION3ALLCp4 - 812

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