9MZZ | pdb_00009mzz

Crystal structure of RIPK1 with compound 36

PDB DOI: https://doi.org/10.2210/pdb9MZZ/pdb

Classification: TRANSFERASE/INHIBITOR
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2025-01-23 Released: 2025-05-28
Deposition Author(s): Lesburg, C.A., Palte, R.L., Maskos, K., Thomsen, M., Lammens, A.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free:
0.272 (Depositor), 0.272 (DCC)
R-Value Work:
0.226 (Depositor), 0.228 (DCC)
R-Value Observed:
0.229 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

The Discovery of Bridged Benzoazepine Amides as Selective Allosteric Modulators of RIPK1.

Chen, J.L., Methot, J.L., Mitcheltree, M.J., Musacchio, A., Corcoran, E.B., Feng, G., Lammens, A., Maskos, K., Palte, R.L., Rickard, M.M., Otte, K.M., Mansueto, M.S., Venkat, S., Sondey, C., Thomsen, M., Lesburg, C.A., Fradera, X., Fell, M.J., DiMauro, E.F., Siliphaivanh, P.

(2025) ACS Med Chem Lett 16: 811-818

PubMed: 40365380 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1021/acsmedchemlett.5c00063
Primary Citation of Related Structures:
9MZX, 9MZY, 9MZZ

PubMed Abstract:
Receptor-interacting protein kinase 1 (RIPK1) plays an essential role in necroptosis, a form of inflammatory, caspase-independent, programmed cell death. Allosteric inhibitors of RIPK1 have been shown to block necroptotic cell death and thus may offer potential therapeutic opportunities across a range of infectious, autoimmune, and neurodegenerative diseases. We report the structure-informed discovery of a novel series of bridged benzoazepine amides as part of our efforts to develop a CNS-penetrant small-molecule inhibitor of RIPK1 with a low projected oral human dose.

Organizational Affiliation

Department of Discovery Chemistry, Merck & Co., Inc., Boston, Massachusetts 02115, United States.

Macromolecule Content

Total Structure Weight: 67.06 kDa
Atom Count: 4,454
Modeled Residue Count: 539
Deposited Residue Count: 576
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Receptor-interacting serine/threonine-protein kinase 1	A, B	288	Homo sapiens	Mutation(s): 0 Gene Names: RIPK1, RIP, RIP1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q13546 (Homo sapiens) Explore Q13546 Go to UniProtKB: Q13546
PHAROS: Q13546 GTEx: ENSG00000137275
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q13546
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BU5 (Subject of Investigation/LOI) Query on A1BU5 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain G [auth B] MOL2 format, chain C [auth A] MOL2 format, chain G [auth B] mmCIF format, chain C [auth A] mmCIF format, chain G [auth B]	C [auth A], G [auth B]	(2S,5S)-4-(3,3-difluoro-2,2-dimethylpropanoyl)-2,3,4,5-tetrahydro-2,5-methanopyrido[3,4-f][1,4]oxazepine-9-carbonitrile C₁₅ H₁₅ F₂ N₃ O₂ SZIVRWFIJWGRAP-ONGXEEELSA-N		Interactions Focus chain C [auth A] Focus chain G [auth B] Interactions & Density Focus chain C [auth A] Focus chain G [auth B]
IOD Query on IOD Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain I [auth B] SDF format, chain E [auth A] SDF format, chain D [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain I [auth B] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain I [auth B] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A]	D [auth A] E [auth A] F [auth A] H [auth B] I [auth B] D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B], K [auth B]	IODIDE ION I XMBWDFGMSWQBCA-UHFFFAOYSA-M		Interactions Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Interactions & Density Focus chain D [auth A] Focus chain E [auth A] Focus chain F [auth A] Focus chain H [auth B] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B]