7A3I

Crystal structure of DPP8 in complex with a 4-oxo-b-lactam based inhibitor, LMC375

PDB DOI: https://doi.org/10.2210/pdb7A3I/pdb

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

Deposited: 2020-08-18 Released: 2021-06-30
Deposition Author(s): Ross, B.H., Huber, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.241
R-Value Work: 0.217
R-Value Observed: 0.218

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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: 313.11 kDa
Atom Count: 19,856
Modelled Residue Count: 2,423
Deposited Residue Count: 2,694
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 8	A, B, C	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
QXH (Subject of Investigation/LOI) Query on QXH Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain M [auth C] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain M [auth C] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain M [auth C]	E [auth A], I [auth B], M [auth C]	~{N}-[3,5-bis[[4-[(4-bromophenyl)methyl]piperazin-1-yl]methyl]phenyl]-2-ethyl-2-methanoyl-butanamide C₃₇ H₄₇ Br₂ N₅ O₂ FVBNIXZASNLFMF-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain M [auth C]
TMO Query on TMO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain H [auth B] SDF format, chain L [auth C] MOL2 format, chain D [auth A] MOL2 format, chain H [auth B] MOL2 format, chain L [auth C] mmCIF format, chain D [auth A] mmCIF format, chain H [auth B] mmCIF format, chain L [auth C]	D [auth A], H [auth B], L [auth C]	trimethylamine oxide C₃ H₉ N O UYPYRKYUKCHHIB-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C] Interactions & Density Focus chain D [auth A] Focus chain H [auth B] Focus chain L [auth C]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain O [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain O [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain O [auth C]	G [auth A], K [auth B], O [auth C]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain O [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain J [auth B] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain J [auth B] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain J [auth B] mmCIF format, chain N [auth C]	F [auth A], J [auth B], N [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C] Interactions & Density Focus chain F [auth A] Focus chain J [auth B] Focus chain N [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.80 Å
R-Value Free: 0.241
R-Value Work: 0.217
R-Value Observed: 0.218
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 163.649	α = 90
b = 252.318	β = 90
c = 259.962	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2021-06-30

Deposition Author(s):

Ross, B.H.

Huber, R.

Revision History (Full details and data files)

Version 1.0: 2021-06-30
Type: Initial release
Version 1.1: 2024-01-31
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-10-16
Changes: Structure summary