7A3K

Crystal structure of DPP8 in complex with a b-lactam based inhibitor, A296.1

PDB DOI: https://doi.org/10.2210/pdb7A3K/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2020-08-18 Released: 2021-07-07
Deposition Author(s): Ross, B.H., Huber, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.65 Å
R-Value Free: 0.244
R-Value Work: 0.217
R-Value Observed: 0.219

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery and Development of 4-Oxo-beta-Lactams as Novel Inhibitors of Dipeptidyl Peptidases 8 and 9

Fehr, L., Carvalho, L.A.R., Ross, B.H., Lum, K., Vieira, A.C., Kiefersauer, R., Geiss-Friedlander, R., Kaiser, M., Rodrigues, T., Lucas, S.D., Cravatt, B.F., Huber, R., Moreira, R.

To be published.

Macromolecule Content

Total Structure Weight: 312.27 kDa
Atom Count: 20,291
Modelled Residue Count: 2,462
Deposited Residue Count: 2,694
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dipeptidyl peptidase 8	A [auth C], B [auth A], C [auth B]	898	Homo sapiens	Mutation(s): 0 Gene Names: DPP8, DPRP1, MSTP097, MSTP135, MSTP141 EC: 3.4.14.5
UniProt & NIH Common Fund Data Resources
Find proteins for Q6V1X1 (Homo sapiens) Explore Q6V1X1 Go to UniProtKB: Q6V1X1
PHAROS: Q6V1X1 GTEx: ENSG00000074603
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6V1X1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
QX8 (Subject of Investigation/LOI) Query on QX8 Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain O [auth A] SDF format, chain T [auth B] MOL2 format, chain J [auth C] MOL2 format, chain O [auth A] MOL2 format, chain T [auth B] mmCIF format, chain J [auth C] mmCIF format, chain O [auth A] mmCIF format, chain T [auth B]	J [auth C], O [auth A], T [auth B]	1-[3-[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]azetidin-2-one C₂₁ H₂₄ Br N₃ O UKZMZNGKMQQUCK-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain O [auth A] Focus chain T [auth B] Interactions & Density Focus chain J [auth C] Focus chain O [auth A] Focus chain T [auth B]
TMO Query on TMO Download Ideal Coordinates CCD File SDF format, chain D [auth C] SDF format, chain K [auth A] SDF format, chain P [auth B] MOL2 format, chain D [auth C] MOL2 format, chain K [auth A] MOL2 format, chain P [auth B] mmCIF format, chain D [auth C] mmCIF format, chain K [auth A] mmCIF format, chain P [auth B]	D [auth C], K [auth A], P [auth B]	trimethylamine oxide C₃ H₉ N O UYPYRKYUKCHHIB-UHFFFAOYSA-N		Interactions Focus chain D [auth C] Focus chain K [auth A] Focus chain P [auth B] Interactions & Density Focus chain D [auth C] Focus chain K [auth A] Focus chain P [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain E [auth C] SDF format, chain F [auth C] SDF format, chain G [auth C] SDF format, chain H [auth C] SDF format, chain L [auth A] SDF format, chain M [auth A] SDF format, chain Q [auth B] SDF format, chain R [auth B] MOL2 format, chain E [auth C] MOL2 format, chain F [auth C] MOL2 format, chain G [auth C] MOL2 format, chain H [auth C] MOL2 format, chain L [auth A] MOL2 format, chain M [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] mmCIF format, chain E [auth C] mmCIF format, chain F [auth C] mmCIF format, chain G [auth C] mmCIF format, chain H [auth C] mmCIF format, chain L [auth A] mmCIF format, chain M [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B]	E [auth C] F [auth C] G [auth C] H [auth C] L [auth A] E [auth C], F [auth C], G [auth C], H [auth C], L [auth A], M [auth A], Q [auth B], R [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B] Interactions & Density Focus chain E [auth C] Focus chain F [auth C] Focus chain G [auth C] Focus chain H [auth C] Focus chain L [auth A] Focus chain M [auth A] Focus chain Q [auth B] Focus chain R [auth B]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth C] SDF format, chain N [auth A] SDF format, chain S [auth B] MOL2 format, chain I [auth C] MOL2 format, chain N [auth A] MOL2 format, chain S [auth B] mmCIF format, chain I [auth C] mmCIF format, chain N [auth A] mmCIF format, chain S [auth B]	I [auth C], N [auth A], S [auth B]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth C] Focus chain N [auth A] Focus chain S [auth B] Interactions & Density Focus chain I [auth C] Focus chain N [auth A] Focus chain S [auth B]