9GON | pdb_00009gon

Crystal structure of DPP9 in complex with sulphostin

PDB DOI: https://doi.org/10.2210/pdb9GON/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-05 Released: 2025-07-16
Deposition Author(s): 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 Organization(s): German Research Foundation (DFG)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.206 (Depositor), 0.282 (DCC)
R-Value Work:
0.163 (Depositor)
R-Value Observed:
0.164 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Sulphostin-inspired N-phosphonopiperidones as selective covalent DPP8 and DPP9 inhibitors.

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.

(2025) Nat Commun 16: 3208-3208

PubMed: 40180908 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-58493-z
Primary Citation Related Structures:
9GOC, 9GOD, 9GOH, 9GON

PubMed Abstract:
Covalent chemical probes and drugs combine unique pharmacologic properties with the availability of straightforward compound profiling technologies via chemoproteomic platforms. These advantages have fostered the development of suitable electrophilic "warheads" for systematic covalent chemical probe discovery. Despite undisputable advances in the last years, the targeted development of proteome-wide selective covalent probes remains a challenge for dipeptidyl peptidase (DPP) 8 and 9 (DPP8/9), intracellular serine hydrolases of the pharmacologically relevant dipeptidyl peptidase 4 activity/structure homologues (DASH) family. Here, we show the exploration of the natural product Sulphostin, a DPP4 inhibitor, as a starting point for DPP8/9 inhibitor development. The generation of Sulphostin-inspired N-phosphonopiperidones leads to derivatives with improved DPP8/9 inhibitory potency, an enhanced proteome-wide selectivity and confirmed DPP8/9 engagement in cells, thereby representing that structural fine-tuning of the warhead's leaving group may represent a straightforward strategy for achieving target selectivity in exoproteases such as DPPs.

Organizational Affiliation

Chemical Biology, Center of Medical Biotechnology, Faculty of Biology, University Duisburg-Essen, Essen, Germany.

Macromolecule Content

Total Structure Weight: 396.25 kDa
Atom Count: 30,750
Modeled Residue Count: 3,372
Deposited Residue Count: 3,404
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 9	A, B, C, D	851	Homo sapiens	Mutation(s): 0 Gene Names: DPP9, DPRP2 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q86TI2 (Homo sapiens) Explore Q86TI2 Go to UniProtKB: Q86TI2
PHAROS: Q86TI2 GTEx: ENSG00000142002
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q86TI2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1INF (Subject of Investigation/LOI) Query on A1INF Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] SDF format, chain DB [auth C] SDF format, chain E [auth A] SDF format, chain EC [auth D] MOL2 format, chain BA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain E [auth A] MOL2 format, chain EC [auth D] mmCIF format, chain BA [auth B] mmCIF format, chain DB [auth C] mmCIF format, chain E [auth A] mmCIF format, chain EC [auth D]	BA [auth B], DB [auth C], E [auth A], EC [auth D]	azanyl-oxidanylidene-(sulfoamino)phosphanium H₄ N₂ O₄ P S UGZLMCWNUKYQNY-UHFFFAOYSA-O		Interactions Focus chain BA [auth B] Focus chain DB [auth C] Focus chain E [auth A] Focus chain EC [auth D] Interactions & Density Focus chain BA [auth B] Focus chain DB [auth C] Focus chain E [auth A] Focus chain EC [auth D]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain EB [auth C] MOL2 format, chain EB [auth C] mmCIF format, chain EB [auth C]	EB [auth C]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain EB [auth C] Interactions & Density Focus chain EB [auth C]
PEG Query on PEG Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain GC [auth D] SDF format, chain JA [auth B] SDF format, chain DA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain GC [auth D] MOL2 format, chain JA [auth B] MOL2 format, chain DA [auth B] mmCIF format, chain F [auth A] mmCIF format, chain GC [auth D] mmCIF format, chain JA [auth B] mmCIF format, chain DA [auth B]	DA [auth B], F [auth A], GC [auth D], JA [auth B]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain DA [auth B] Focus chain F [auth A] Focus chain GC [auth D] Focus chain JA [auth B] Interactions & Density Focus chain DA [auth B] Focus chain F [auth A] Focus chain GC [auth D] Focus chain JA [auth B]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain BB [auth B] SDF format, chain BC [auth C] SDF format, chain CA [auth B] SDF format, chain EA [auth B] SDF format, chain FA [auth B] SDF format, chain FB [auth C] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain GB [auth C] SDF format, chain HB [auth C] SDF format, chain HC [auth D] SDF format, chain I [auth A] SDF format, chain IB [auth C] SDF format, chain IC [auth D] SDF format, chain JC [auth D] SDF format, chain K [auth A] SDF format, chain KA [auth B] SDF format, chain KB [auth C] SDF format, chain KC [auth D] SDF format, chain L [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth C] SDF format, chain LC [auth D] SDF format, chain MA [auth B] SDF format, chain MB [auth C] SDF format, chain MC [auth D] SDF format, chain N [auth A] SDF format, chain NA [auth B] SDF format, chain NB [auth C] SDF format, chain NC [auth D] SDF format, chain O [auth A] SDF format, chain OA [auth B] SDF format, chain OB [auth C] SDF format, chain OC [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth B] SDF format, chain PB [auth C] SDF format, chain PC [auth D] SDF format, chain Q [auth A] SDF format, chain QA [auth B] SDF format, chain QB [auth C] SDF format, chain QC [auth D] SDF format, chain RA [auth B] SDF format, chain RB [auth C] SDF format, chain RC [auth D] SDF format, chain S [auth A] SDF format, chain SA [auth B] SDF format, chain SB [auth C] SDF format, chain SC [auth D] SDF format, chain T [auth A] SDF format, chain TA [auth B] SDF format, chain TC [auth D] SDF format, chain U [auth A] SDF format, chain UA [auth B] SDF format, chain UB [auth C] SDF format, chain V [auth A] SDF format, chain VA [auth B] SDF format, chain VB [auth C] SDF format, chain WA [auth B] SDF format, chain WB [auth C] SDF format, chain XA [auth B] SDF format, chain XB [auth C] SDF format, chain YB [auth C] SDF format, chain ZA [auth B] SDF format, chain W [auth A] SDF format, chain TB [auth C] SDF format, chain R [auth A] SDF format, chain M [auth A] SDF format, chain JB [auth C] SDF format, chain J [auth A] SDF format, chain H [auth A] MOL2 format, chain BB [auth B] MOL2 format, chain BC [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain FA [auth B] MOL2 format, chain FB [auth C] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain GB [auth C] MOL2 format, chain HB [auth C] MOL2 format, chain HC [auth D] MOL2 format, chain I [auth A] MOL2 format, chain IB [auth C] MOL2 format, chain IC [auth D] MOL2 format, chain JC [auth D] MOL2 format, chain K [auth A] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth C] MOL2 format, chain KC [auth D] MOL2 format, chain L [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth C] MOL2 format, chain LC [auth D] MOL2 format, chain MA [auth B] MOL2 format, chain MB [auth C] MOL2 format, chain MC [auth D] MOL2 format, chain N [auth A] MOL2 format, chain NA [auth B] MOL2 format, chain NB [auth C] MOL2 format, chain NC [auth D] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth B] MOL2 format, chain OB [auth C] MOL2 format, chain OC [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth B] MOL2 format, chain PB [auth C] MOL2 format, chain PC [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain QA [auth B] MOL2 format, chain QB [auth C] MOL2 format, chain QC [auth D] MOL2 format, chain RA [auth B] MOL2 format, chain RB [auth C] MOL2 format, chain RC [auth D] MOL2 format, chain S [auth A] MOL2 format, chain SA [auth B] MOL2 format, chain SB [auth C] MOL2 format, chain SC [auth D] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth B] MOL2 format, chain TC [auth D] MOL2 format, chain U [auth A] MOL2 format, chain UA [auth B] MOL2 format, chain UB [auth C] MOL2 format, chain V [auth A] MOL2 format, chain VA [auth B] MOL2 format, chain VB [auth C] MOL2 format, chain WA [auth B] MOL2 format, chain WB [auth C] MOL2 format, chain XA [auth B] MOL2 format, chain XB [auth C] MOL2 format, chain YB [auth C] MOL2 format, chain ZA [auth B] MOL2 format, chain W [auth A] MOL2 format, chain TB [auth C] MOL2 format, chain R [auth A] MOL2 format, chain M [auth A] MOL2 format, chain JB [auth C] MOL2 format, chain J [auth A] MOL2 format, chain H [auth A] mmCIF format, chain BB [auth B] mmCIF format, chain BC [auth C] mmCIF format, chain CA [auth B] mmCIF format, chain EA [auth B] mmCIF format, chain FA [auth B] mmCIF format, chain FB [auth C] mmCIF format, chain G [auth A] mmCIF format, chain GA [auth B] mmCIF format, chain GB [auth C] mmCIF format, chain HB [auth C] mmCIF format, chain HC [auth D] mmCIF format, chain I [auth A] mmCIF format, chain IB [auth C] mmCIF format, chain IC [auth D] mmCIF format, chain JC [auth D] mmCIF format, chain K [auth A] mmCIF format, chain KA [auth B] mmCIF format, chain KB [auth C] mmCIF format, chain KC [auth D] mmCIF format, chain L [auth A] mmCIF format, chain LA [auth B] mmCIF format, chain LB [auth C] mmCIF format, chain LC [auth D] mmCIF format, chain MA [auth B] mmCIF format, chain MB [auth C] mmCIF format, chain MC [auth D] mmCIF format, chain N [auth A] mmCIF format, chain NA [auth B] mmCIF format, chain NB [auth C] mmCIF format, chain NC [auth D] mmCIF format, chain O [auth A] mmCIF format, chain OA [auth B] mmCIF format, chain OB [auth C] mmCIF format, chain OC [auth D] mmCIF format, chain P [auth A] mmCIF format, chain PA [auth B] mmCIF format, chain PB [auth C] mmCIF format, chain PC [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain QA [auth B] mmCIF format, chain QB [auth C] mmCIF format, chain QC [auth D] mmCIF format, chain RA [auth B] mmCIF format, chain RB [auth C] mmCIF format, chain RC [auth D] mmCIF format, chain S [auth A] mmCIF format, chain SA [auth B] mmCIF format, chain SB [auth C] mmCIF format, chain SC [auth D] mmCIF format, chain T [auth A] mmCIF format, chain TA [auth B] mmCIF format, chain TC [auth D] mmCIF format, chain U [auth A] mmCIF format, chain UA [auth B] mmCIF format, chain UB [auth C] mmCIF format, chain V [auth A] mmCIF format, chain VA [auth B] mmCIF format, chain VB [auth C] mmCIF format, chain WA [auth B] mmCIF format, chain WB [auth C] mmCIF format, chain XA [auth B] mmCIF format, chain XB [auth C] mmCIF format, chain YB [auth C] mmCIF format, chain ZA [auth B] mmCIF format, chain W [auth A] mmCIF format, chain TB [auth C] mmCIF format, chain R [auth A] mmCIF format, chain M [auth A] mmCIF format, chain JB [auth C] mmCIF format, chain J [auth A] mmCIF format, chain H [auth A]	BB [auth B] BC [auth C] CA [auth B] EA [auth B] FA [auth B] BB [auth B], BC [auth C], CA [auth B], EA [auth B], FA [auth B], FB [auth C], G [auth A], GA [auth B], GB [auth C], H [auth A], HB [auth C], HC [auth D], I [auth A], IB [auth C], IC [auth D], J [auth A], JB [auth C], JC [auth D], K [auth A], KA [auth B], KB [auth C], KC [auth D], L [auth A], LA [auth B], LB [auth C], LC [auth D], M [auth A], MA [auth B], MB [auth C], MC [auth D], N [auth A], NA [auth B], NB [auth C], NC [auth D], O [auth A], OA [auth B], OB [auth C], OC [auth D], P [auth A], PA [auth B], PB [auth C], PC [auth D], Q [auth A], QA [auth B], QB [auth C], QC [auth D], R [auth A], RA [auth B], RB [auth C], RC [auth D], S [auth A], SA [auth B], SB [auth C], SC [auth D], T [auth A], TA [auth B], TB [auth C], TC [auth D], U [auth A], UA [auth B], UB [auth C], V [auth A], VA [auth B], VB [auth C], W [auth A], WA [auth B], WB [auth C], XA [auth B], XB [auth C], YB [auth C], ZA [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain BB [auth B] Focus chain BC [auth C] Focus chain CA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HB [auth C] Focus chain HC [auth D] Focus chain I [auth A] Focus chain IB [auth C] Focus chain IC [auth D] Focus chain J [auth A] Focus chain JB [auth C] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain RC [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain TC [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain YB [auth C] Focus chain ZA [auth B] Interactions & Density Focus chain BB [auth B] Focus chain BC [auth C] Focus chain CA [auth B] Focus chain EA [auth B] Focus chain FA [auth B] Focus chain FB [auth C] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth C] Focus chain H [auth A] Focus chain HB [auth C] Focus chain HC [auth D] Focus chain I [auth A] Focus chain IB [auth C] Focus chain IC [auth D] Focus chain J [auth A] Focus chain JB [auth C] Focus chain JC [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth C] Focus chain KC [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth C] Focus chain LC [auth D] Focus chain M [auth A] Focus chain MA [auth B] Focus chain MB [auth C] Focus chain MC [auth D] Focus chain N [auth A] Focus chain NA [auth B] Focus chain NB [auth C] Focus chain NC [auth D] Focus chain O [auth A] Focus chain OA [auth B] Focus chain OB [auth C] Focus chain OC [auth D] Focus chain P [auth A] Focus chain PA [auth B] Focus chain PB [auth C] Focus chain PC [auth D] Focus chain Q [auth A] Focus chain QA [auth B] Focus chain QB [auth C] Focus chain QC [auth D] Focus chain R [auth A] Focus chain RA [auth B] Focus chain RB [auth C] Focus chain RC [auth D] Focus chain S [auth A] Focus chain SA [auth B] Focus chain SB [auth C] Focus chain SC [auth D] Focus chain T [auth A] Focus chain TA [auth B] Focus chain TB [auth C] Focus chain TC [auth D] Focus chain U [auth A] Focus chain UA [auth B] Focus chain UB [auth C] Focus chain V [auth A] Focus chain VA [auth B] Focus chain VB [auth C] Focus chain W [auth A] Focus chain WA [auth B] Focus chain WB [auth C] Focus chain XA [auth B] Focus chain XB [auth C] Focus chain YB [auth C] Focus chain ZA [auth B]
CL Query on CL Download:Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain AB [auth B] SDF format, chain AC [auth C] SDF format, chain CC [auth C] SDF format, chain HA [auth B] SDF format, chain VC [auth D] SDF format, chain X [auth A] SDF format, chain Y [auth A] SDF format, chain YA [auth B] SDF format, chain ZB [auth C] SDF format, chain UC [auth D] SDF format, chain IA [auth B] MOL2 format, chain AA [auth A] MOL2 format, chain AB [auth B] MOL2 format, chain AC [auth C] MOL2 format, chain CC [auth C] MOL2 format, chain HA [auth B] MOL2 format, chain VC [auth D] MOL2 format, chain X [auth A] MOL2 format, chain Y [auth A] MOL2 format, chain YA [auth B] MOL2 format, chain ZB [auth C] MOL2 format, chain UC [auth D] MOL2 format, chain IA [auth B] mmCIF format, chain AA [auth A] mmCIF format, chain AB [auth B] mmCIF format, chain AC [auth C] mmCIF format, chain CC [auth C] mmCIF format, chain HA [auth B] mmCIF format, chain VC [auth D] mmCIF format, chain X [auth A] mmCIF format, chain Y [auth A] mmCIF format, chain YA [auth B] mmCIF format, chain ZB [auth C] mmCIF format, chain UC [auth D] mmCIF format, chain IA [auth B]	AA [auth A] AB [auth B] AC [auth C] CC [auth C] HA [auth B] AA [auth A], AB [auth B], AC [auth C], CC [auth C], HA [auth B], IA [auth B], UC [auth D], VC [auth D], X [auth A], Y [auth A], YA [auth B], ZB [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth C] Focus chain CC [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain UC [auth D] Focus chain VC [auth D] Focus chain X [auth A] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain ZB [auth C] Interactions & Density Focus chain AA [auth A] Focus chain AB [auth B] Focus chain AC [auth C] Focus chain CC [auth C] Focus chain HA [auth B] Focus chain IA [auth B] Focus chain UC [auth D] Focus chain VC [auth D] Focus chain X [auth A] Focus chain Y [auth A] Focus chain YA [auth B] Focus chain ZB [auth C]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain CB [auth B] SDF format, chain FC [auth D] SDF format, chain WC [auth D] SDF format, chain Z [auth A] SDF format, chain DC [auth C] MOL2 format, chain CB [auth B] MOL2 format, chain FC [auth D] MOL2 format, chain WC [auth D] MOL2 format, chain Z [auth A] MOL2 format, chain DC [auth C] mmCIF format, chain CB [auth B] mmCIF format, chain FC [auth D] mmCIF format, chain WC [auth D] mmCIF format, chain Z [auth A] mmCIF format, chain DC [auth C]	CB [auth B], DC [auth C], FC [auth D], WC [auth D], Z [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain CB [auth B] Focus chain DC [auth C] Focus chain FC [auth D] Focus chain WC [auth D] Focus chain Z [auth A] Interactions & Density Focus chain CB [auth B] Focus chain DC [auth C] Focus chain FC [auth D] Focus chain WC [auth D] Focus chain Z [auth A]