PDB-9gon: Crystal structure of DPP9 in complex with sulphostin

ID or keywords:

Entry

Database: PDB / ID: 9gon

Title

Crystal structure of DPP9 in complex with sulphostin

Components

Dipeptidyl peptidase 9

Keywords

TRANSFERASE / 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 ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.89 Å

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. ...

Funding support

Germany, 1items

Citation

Journal: 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

Deposition	Sep 5, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jul 16, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	9gon.cif.gz	1.4 MB	Display	PDBx/mmCIF format
PDB format	pdb9gon.ent.gz		Display	PDB format
PDBx/mmJSON format	9gon.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	9gon_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	9gon_full_validation.pdf.gz	1.9 MB	Display
Data in XML	9gon_validation.xml.gz	163.8 KB	Display
Data in CIF	9gon_validation.cif.gz	225.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/go/9gon ftp://data.pdbj.org/pub/pdb/validation_reports/go/9gon	HTTPS FTP

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Related structure data

Related structure data	9gocC 9godC 9gohC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (5)

Deposited unit

A: Dipeptidyl peptidase 9

B: Dipeptidyl peptidase 9

C: Dipeptidyl peptidase 9

D: Dipeptidyl peptidase 9

hetero molecules

396 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Dipeptidyl peptidase 9

B: Dipeptidyl peptidase 9

hetero molecules

defined by author
198 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Dipeptidyl peptidase 9

D: Dipeptidyl peptidase 9

hetero molecules

defined by author
198 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	88.799, 106.683, 121.143
Angle α, β, γ (deg.)	65.05, 70.82, 76.58
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID
1	1
2	2
3	3
4	4
5	5
6	6

/ NCS ensembles :

ID
1
2
3
4
5
6

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Protein , 1 types, 4 molecules ABCD

#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

#1: Protein

Dipeptidyl peptidase 9 / DP9 / Dipeptidyl peptidase IV-related protein 2 / DPRP-2 / Dipeptidyl peptidase IX / DPP IX / ...

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

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Non-polymers , 7 types, 2470 molecules

#2: Chemical	ChemComp-A1INF / azanyl-oxidanylidene-(sulfoamino)phosphanium Mass: 159.082 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: H₄N₂O₄PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	... ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 71 / Source method: obtained synthetically / Formula: C₂H₆O₂
#5: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: Cl
#6: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Na
#7: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#8: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 2373 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	Y
Has protein modification	Y

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.5 Å³/Da / Density % sol: 50.88 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / Details: 20% (w/v) PEG 2000 MME, 0.1M Tris pH 6.75

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.9998 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 24, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9998 Å / Relative weight: 1
Reflection	Resolution: 1.89→90.21 Å / Num. obs: 289674 / % possible obs: 96.3 % / Redundancy: 2.2 % / CC_1/2: 0.99 / Net I/σ(I): 5.3
Reflection shell	Resolution: 1.89→1.93 Å / Num. unique obs: 14469 / CC_1/2: 0.96

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Processing

Software

Name	Version	Classification
autoPROC		data reduction
XDS	(VERSION Jan 31	data reduction
autoPROC	(Version 1.1.7)	data scaling
Aimless		data scaling
REFMAC	5.8.0267	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.89→90.21 Å / Cor.coef. F_o:F_c: 0.971 / Cor.coef. F_o:F_c free: 0.935 / SU B: 7.389 / SU ML: 0.107 / Cross valid method: THROUGHOUT / ESU R: 0.134 / ESU R Free: 0.129 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20597	2295	0.8 %	RANDOM
R_work	0.16339	-	-	-
obs	0.16372	287379	96.21 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 39.084 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.26 Å²	-0.04 Å²	-0.92 Å²
2-	-	-0.97 Å²	0.3 Å²
3-	-	-	-0.31 Å²

Refinement step

Cycle: LAST / Resolution: 1.89→90.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	27262	0	371	2373	30006

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	28765
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.017	26312
X-RAY DIFFRACTION	r_angle_refined_deg	1.473	1.647	39096
X-RAY DIFFRACTION	r_angle_other_deg	1.282	1.569	60645
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.258	5	3561
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.876	22.143	1484
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.999	15	4518
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	21.839	15	155
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	3527
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	32977
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	6853
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.243	2.321	13971
X-RAY DIFFRACTION	r_mcbond_other	1.242	2.321	13970
X-RAY DIFFRACTION	r_mcangle_it	2.062	3.473	17623
X-RAY DIFFRACTION	r_mcangle_other	2.062	3.473	17624
X-RAY DIFFRACTION	r_scbond_it	1.599	2.513	14794
X-RAY DIFFRACTION	r_scbond_other	1.599	2.513	14795
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	2.578	3.661	21474
X-RAY DIFFRACTION	r_long_range_B_refined	5.452	27.431	30894
X-RAY DIFFRACTION	r_long_range_B_other	5.359	26.827	30413
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	9998	0.04
1	2	B	9998	0.04
2	1	A	10107	0.03
2	2	C	10107	0.03
3	1	A	9972	0.03
3	2	D	9972	0.03
4	1	B	10057	0.04
4	2	C	10057	0.04
5	1	B	9972	0.04
5	2	D	9972	0.04
6	1	C	9961	0.03
6	2	D	9961	0.03

LS refinement shell

Resolution: 1.894→1.944 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.291	150	-
R_work	0.278	21173	-
obs	-	-	95.68 %

Refinement TLS params.

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

ID	L11 (°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)
1	1.2023	0.1614	0.6345	1.1727	0.164	0.6705	0.0161	0.0365	0.0429	0.0341	-0.0085	-0.0874	-0.0277	0.0513	-0.0075	0.0056	-0.0042	-0.0008	0.0073	0.009	0.0397	12.324	-47.845	-52.168
2	0.8799	0.324	0.0106	1.0602	0.198	0.6476	0.0183	-0.0811	0.0558	0.0945	-0.0256	0.1047	0.0141	-0.1221	0.0074	0.0174	0.011	0.0103	0.0496	0.0136	0.0945	-22.657	-39.211	-50.71
3	1.6245	-0.7743	1.3901	4.1853	-2.4224	2.0028	0.0786	-0.1784	-0.1102	0.0717	-0.0012	0.0213	0.0227	-0.1115	-0.0774	0.0451	0.0032	0.0263	0.0325	0.0091	0.1018	-8.44	-66.003	-52.356
4	1.1597	0.0642	-0.1022	1.6047	-0.1337	0.3784	0.0466	-0.0747	-0.043	0.1075	-0.0342	-0.2336	0.029	0.0896	-0.0123	0.0538	-0.0094	-0.072	0.0281	0.0168	0.1033	19.615	-81.937	-40.855
5	1.2374	-0.0557	0.2208	0.8584	-0.048	0.626	-0.0226	0.1662	-0.0083	-0.0377	0.009	-0.0346	0.0305	-0.0073	0.0135	0.0544	-0.0157	-0.0247	0.0316	0.0208	0.0848	-2.599	-107.041	-54.189
6	1.7513	0.406	-0.0091	4.4994	-3.3236	2.5055	-0.0772	0.1621	0.0005	-0.0783	0.0387	-0.0501	0.0401	-0.0041	0.0386	0.0861	-0.0092	-0.037	0.0255	-0.0033	0.0975	-5.687	-77.161	-50.04
7	0.7664	-0.1924	0.4614	1.1846	0.1953	0.9765	-0.039	-0.0507	0.1485	-0.0138	0.0189	-0.0912	-0.1022	0.1116	0.0201	0.0326	-0.0233	-0.0241	0.0631	0.0088	0.0818	30.043	-57.617	-97.637
8	0.7288	0.1239	0.1628	0.9618	0.5408	1.1647	0.018	-0.1086	-0.0019	0.1192	-0.0366	0.1101	0.1474	-0.2068	0.0187	0.0955	-0.0244	-0.047	0.076	0.0358	0.0887	-3.532	-64.548	-108.46
9	1.1832	-0.8718	2.3389	3.4534	-3.0744	5.2921	0.098	-0.1253	-0.0369	-0.1041	-0.0272	0.094	0.227	-0.155	-0.0707	0.0865	0.0238	-0.013	0.0957	0.0468	0.1147	20.734	-82.743	-104.06
10	1.1576	-0.0738	0.3346	1.4486	-0.2315	0.6217	-0.0018	-0.0735	0.0401	0.0401	-0.0175	-0.1242	-0.0087	0.0786	0.0192	0.0272	-0.0019	-0.0131	0.0799	0.0381	0.0645	47.457	-85.996	-82.601
11	1.4512	0.2743	0.2467	1.1199	0.2006	0.829	-0.1462	0.3048	-0.1587	-0.3943	0.1702	-0.1429	0.1008	0.0899	-0.0239	0.2918	-0.043	0.0223	0.1577	-0.0043	0.1955	45.789	-116.08	-101.447
12	1.1689	-0.2542	1.359	5.4149	-3.0456	2.9992	-0.043	-0.0163	-0.0702	-0.4153	0.0817	-0.0468	0.1594	-0.0878	-0.0388	0.1279	0.0136	-0.0117	0.1223	0.0001	0.1087	27.458	-91.884	-100.617

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	20 - 45
2	X-RAY DIFFRACTION	1	B	603 - 865
3	X-RAY DIFFRACTION	2	B	46 - 285
4	X-RAY DIFFRACTION	2	B	311 - 602
5	X-RAY DIFFRACTION	3	B	286 - 310
6	X-RAY DIFFRACTION	4	A	22 - 45
7	X-RAY DIFFRACTION	4	A	603 - 865
8	X-RAY DIFFRACTION	5	A	46 - 285
9	X-RAY DIFFRACTION	5	A	311 - 602
10	X-RAY DIFFRACTION	6	A	286 - 310
11	X-RAY DIFFRACTION	7	C	21 - 45
12	X-RAY DIFFRACTION	7	C	603 - 865
13	X-RAY DIFFRACTION	8	C	46 - 285
14	X-RAY DIFFRACTION	8	C	311 - 602
15	X-RAY DIFFRACTION	9	C	286 - 310
16	X-RAY DIFFRACTION	10	D	22 - 45
17	X-RAY DIFFRACTION	10	D	603 - 864
18	X-RAY DIFFRACTION	11	D	46 - 285
19	X-RAY DIFFRACTION	11	D	311 - 602
20	X-RAY DIFFRACTION	12	D	286 - 310

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