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- PDB-9q6l: Human prolyl endopeptidase (PREP) - complex with KT-2-197 -

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Basic information

Entry
Database: PDB / ID: 9q6l
TitleHuman prolyl endopeptidase (PREP) - complex with KT-2-197
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: 1.66 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
C: Prolyl endopeptidase
A: Prolyl endopeptidase
B: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)249,20867
Polymers242,5543
Non-polymers6,65464
Water29,9231661
1
C: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,77732
Polymers80,8511
Non-polymers2,92631
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,99321
Polymers80,8511
Non-polymers2,14220
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
B: Prolyl endopeptidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,43814
Polymers80,8511
Non-polymers1,58613
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)103.445, 66.247, 156.2
Angle α, β, γ (deg.)90, 102.004, 90
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 3 molecules CAB

#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 , 8 types, 1725 molecules

#2: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 18 / Source method: obtained synthetically / Formula: CNS
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 26 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-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


Mass: 426.899 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C21H23ClN6O2 / Feature type: SUBJECT OF INVESTIGATION
#7: 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.: 2 / Source method: obtained synthetically / Formula: C11H26N2O6 / Comment: pH buffer*YM
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1661 / 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: 2.16 Å3/Da / Density % sol: 43.01 %
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: 0.919901 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 23, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919901 Å / Relative weight: 1
ReflectionResolution: 1.66→34.5 Å / Num. obs: 184521 / % possible obs: 95.2 % / Redundancy: 7 % / Biso Wilson estimate: 13.9 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.248 / Rpim(I) all: 0.1 / Rrim(I) all: 0.267 / Net I/σ(I): 6.5
Reflection shellResolution: 1.66→1.84 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.425 / Mean I/σ(I) obs: 1.4 / Num. unique obs: 9226 / CC1/2: 0.34 / Rpim(I) all: 0.589 / Rrim(I) all: 1.544 / % possible all: 55.6

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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: 1.66→34.5 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.34 / SU ML: 0.104 / Cross valid method: FREE R-VALUE / ESU R: 0.132 / ESU R Free: 0.132
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2159 9156 4.962 %
Rwork0.1616 175365 -
all0.164 --
obs-184521 75.401 %
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: 18.612 Å2
Baniso -1Baniso -2Baniso -3
1-0.008 Å2-0 Å2-0.132 Å2
2--0.069 Å20 Å2
3----0.019 Å2
Refinement stepCycle: LAST / Resolution: 1.66→34.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17019 0 419 1661 19099
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.01217960
X-RAY DIFFRACTIONr_bond_other_d0.0010.01616485
X-RAY DIFFRACTIONr_angle_refined_deg2.3231.81824268
X-RAY DIFFRACTIONr_angle_other_deg0.7761.75938134
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.36252152
X-RAY DIFFRACTIONr_dihedral_angle_2_deg13.231588
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.448102938
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.54510858
X-RAY DIFFRACTIONr_chiral_restr0.1130.22565
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0220848
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024141
X-RAY DIFFRACTIONr_nbd_refined0.2180.23443
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2040.216128
X-RAY DIFFRACTIONr_nbtor_refined0.1910.28637
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0940.29587
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1930.21524
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1370.210
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1630.245
X-RAY DIFFRACTIONr_nbd_other0.2610.2170
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2130.246
X-RAY DIFFRACTIONr_mcbond_it1.3131.0348533
X-RAY DIFFRACTIONr_mcbond_other1.3091.0338529
X-RAY DIFFRACTIONr_mcangle_it1.8931.84410647
X-RAY DIFFRACTIONr_mcangle_other1.8931.84410648
X-RAY DIFFRACTIONr_scbond_it2.5911.339427
X-RAY DIFFRACTIONr_scbond_other2.5911.339428
X-RAY DIFFRACTIONr_scangle_it3.8052.2913604
X-RAY DIFFRACTIONr_scangle_other3.8052.2913605
X-RAY DIFFRACTIONr_lrange_it5.46912.64520611
X-RAY DIFFRACTIONr_lrange_other5.39812.13320233
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.66-1.7020.41260.23279X-RAY DIFFRACTION0.4739
1.702-1.7480.249180.272347X-RAY DIFFRACTION2.0817
1.748-1.7990.2981320.2942221X-RAY DIFFRACTION13.8558
1.799-1.8540.334410.298289X-RAY DIFFRACTION52.6316
1.854-1.9150.2986740.26413230X-RAY DIFFRACTION86.5053
1.915-1.9820.2768080.2414486X-RAY DIFFRACTION98.5248
1.982-2.0560.2517190.21214214X-RAY DIFFRACTION99.4936
2.056-2.140.257470.19713599X-RAY DIFFRACTION99.3834
2.14-2.2340.2346720.16913213X-RAY DIFFRACTION99.7701
2.234-2.3430.2196390.16112535X-RAY DIFFRACTION99.8106
2.343-2.4690.2265730.14812065X-RAY DIFFRACTION99.7947
2.469-2.6180.2155830.14711369X-RAY DIFFRACTION99.9331
2.618-2.7980.2235330.14310726X-RAY DIFFRACTION99.9556
2.798-3.020.2235310.149973X-RAY DIFFRACTION100
3.02-3.3060.24930.1339180X-RAY DIFFRACTION99.9897
3.306-3.6920.1694730.138315X-RAY DIFFRACTION100
3.692-4.2550.1753860.1187361X-RAY DIFFRACTION100
4.255-5.1920.1473150.126314X-RAY DIFFRACTION100
5.192-7.260.2022610.164940X-RAY DIFFRACTION100
7.26-34.50.1931520.1592912X-RAY DIFFRACTION100
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)
10.28350.0264-0.12730.5132-0.16310.54480.0042-0.03330.01920.01360.0077-0.04280.01040.0368-0.01180.00650.003-0.00660.0065-0.00630.010639.64191.644926.8694
20.57030.0841-0.18110.4259-0.01030.4718-0.02670.0022-0.01740.02350.0163-0.0430.03530.02720.01040.00770.0049-0.00570.004-0.00430.010461.63546.804775.81
30.9061-0.3403-0.36460.53680.1780.47210.05280.01790.1319-0.0453-0.0039-0.016-0.0445-0.0414-0.04890.0351-0.0005-0.00030.01770.00290.032291.287236.281623.0949
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLCp4 - 834
2X-RAY DIFFRACTION2ALLAp4 - 820
3X-RAY DIFFRACTION3ALLBp4 - 815

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