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- PDB-9god: Crystal structure of DPP9 in complex with N-phosphono-(S)-3-amino... -

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Basic information

Entry
Database: PDB / ID: 9god
TitleCrystal structure of DPP9 in complex with N-phosphono-(S)-3-aminopiperidine-2-one-based inhibitor
ComponentsDipeptidyl peptidase 9
KeywordsTRANSFERASE / Dipeptidyl peptidase / dipeptidyl peptidase inhibitor
Function / homology
Function and homology information


dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding ...dipeptidyl-peptidase IV / dipeptidyl-peptidase activity / negative regulation of programmed cell death / pyroptotic inflammatory response / cell leading edge / aminopeptidase activity / serine-type peptidase activity / microtubule / proteolysis / identical protein binding / nucleus / cytosol
Similarity search - Function
Dipeptidyl peptidase 8 /9 ,N-terminal / Dipeptidyl peptidase 8 and 9 N-terminal / : / Dipeptidylpeptidase IV, N-terminal domain / Dipeptidyl peptidase IV (DPP IV) N-terminal region / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
: / Dipeptidyl peptidase 9
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsSewald, L. / Tabak, W.W.A. / Fehr, L. / Zolg, S. / Najdzion, M. / Verhoef, C.J.A. / Podlesainski, D. / Geiss-Friedlander, R. / Lammens, A. / Kaschani, F. ...Sewald, L. / Tabak, W.W.A. / Fehr, L. / Zolg, S. / Najdzion, M. / Verhoef, C.J.A. / Podlesainski, D. / Geiss-Friedlander, R. / Lammens, A. / Kaschani, F. / Hellerschmied, D. / Huber, R. / Kaiser, M.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)CRC1430, Project number 424228829 Germany
CitationJournal: Nat Commun / Year: 2025
Title: Sulphostin-inspired N-phosphonopiperidones as selective covalent DPP8 and DPP9 inhibitors.
Authors: Sewald, L. / Tabak, W.W.A. / Fehr, L. / Zolg, S. / Najdzion, M. / Verhoef, C.J.A. / Podlesainski, D. / Geiss-Friedlander, R. / Lammens, A. / Kaschani, F. / Hellerschmied, D. / Huber, R. / Kaiser, M.
History
DepositionSep 5, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl peptidase 9
B: Dipeptidyl peptidase 9
C: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)393,53945
Polymers390,0944
Non-polymers3,44541
Water11,458636
1
A: Dipeptidyl peptidase 9
D: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,42817
Polymers195,0472
Non-polymers1,38115
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8270 Å2
ΔGint20 kcal/mol
Surface area65680 Å2
MethodPISA
2
B: Dipeptidyl peptidase 9
C: Dipeptidyl peptidase 9
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,11128
Polymers195,0472
Non-polymers2,06426
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10440 Å2
ΔGint51 kcal/mol
Surface area65580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.306, 106.746, 121.482
Angle α, β, γ (deg.)65.24, 71.02, 76.71
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Dipeptidyl peptidase 9 / DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / ...DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / Dipeptidyl peptidase-like protein 9 / DPLP9


Mass: 97523.516 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DPP9, DPRP2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q86TI2, dipeptidyl-peptidase IV
#2: Chemical
ChemComp-A1INH / ethoxy-[2-(4-pentylphenyl)sulfanylethyl]phosphinous acid


Mass: 300.397 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H25O2PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 35 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 636 / Source method: isolated from a natural source / Formula: H2O
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: 2.53 Å3/Da / Density % sol: 51.46 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 18.0% w/v PEG 2K MME; 0.1 M Tris pH 7.25

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.8856 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Jun 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8856 Å / Relative weight: 1
ReflectionResolution: 2.49→106.55 Å / Num. obs: 95210 / % possible obs: 98.7 % / Redundancy: 3.7 % / CC1/2: 0.99 / Net I/σ(I): 5.5
Reflection shellResolution: 2.49→2.74 Å / Num. unique obs: 4826 / CC1/2: 0.68

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Processing

Software
NameVersionClassification
autoPROCdata reduction
XDS(VERSION Jun 30data reduction
autoPROC(Version 1.1.7)data scaling
Aimlessdata scaling
REFMAC5.8.0419refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→106.55 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.242 / SU ML: 0.239 / Cross valid method: THROUGHOUT / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21881 2036 2.1 %RANDOM
Rwork0.17036 ---
obs0.17138 95210 72.31 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.351 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å2-0.01 Å20.11 Å2
2--0.3 Å2-0.22 Å2
3----0.15 Å2
Refinement stepCycle: LAST / Resolution: 2.49→106.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms26205 0 218 636 27059
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01226810
X-RAY DIFFRACTIONr_bond_other_d0.0020.01624457
X-RAY DIFFRACTIONr_angle_refined_deg1.3751.83336370
X-RAY DIFFRACTIONr_angle_other_deg0.5361.73856334
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.22353252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.1375129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.068103948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0680.23811
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0231509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.026291
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.464.97613020
X-RAY DIFFRACTIONr_mcbond_other3.4594.97613020
X-RAY DIFFRACTIONr_mcangle_it5.638.94316268
X-RAY DIFFRACTIONr_mcangle_other5.638.94416269
X-RAY DIFFRACTIONr_scbond_it3.3285.06713790
X-RAY DIFFRACTIONr_scbond_other3.3285.06713791
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.5049.21220103
X-RAY DIFFRACTIONr_long_range_B_refined8.03345.2127643
X-RAY DIFFRACTIONr_long_range_B_other8.03345.2627588
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.49→2.552 Å
RfactorNum. reflection% reflection
Rfree0 0 -
Rwork0.242 97 -
obs--0.97 %

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