9GOH | pdb_00009goh

Crystal structure of DPP4 in complex with sulphostin.

PDB DOI: https://doi.org/10.2210/pdb9GOH/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: 2.38 Å
R-Value Free:
0.285 (Depositor), 0.284 (DCC)
R-Value Work:
0.236 (Depositor), 0.236 (DCC)
R-Value Observed:
0.236 (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 PubMedSearch on PubMed Central
DOI: https://doi.org/10.1038/s41467-025-58493-z
Primary Citation of 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: 176.09 kDa
Atom Count: 12,358
Modeled Residue Count: 1,457
Deposited Residue Count: 1,472
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 4 soluble form	A, B	736	Homo sapiens	Mutation(s): 0 Gene Names: DPP4, ADCP2, CD26 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for P27487 (Homo sapiens) Explore P27487 Go to UniProtKB: P27487
PHAROS: P27487 GTEx: ENSG00000197635
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P27487
Glycosylation
Glycosylation Sites: 7	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P27487-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	3		N-Glycosylation	Interactions Focus chain C Interactions & Density Focus chain C

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	6		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
A1INF (Subject of Investigation/LOI) Query on A1INF Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain T [auth B] MOL2 format, chain K [auth A] MOL2 format, chain T [auth B] mmCIF format, chain K [auth A] mmCIF format, chain T [auth B]	K [auth A], T [auth B]	azanyl-oxidanylidene-(sulfoamino)phosphanium H₄ N₂ O₄ P S UGZLMCWNUKYQNY-UHFFFAOYSA-O		Interactions Focus chain K [auth A] Focus chain T [auth B] Interactions & Density Focus chain K [auth A] Focus chain T [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain U [auth B] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain U [auth B] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain U [auth B] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	L [auth A], M [auth A], U [auth B], V [auth B], W [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain L [auth A] Focus chain M [auth A] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]