5T8O | pdb_00005t8o

Crystal structure of murine NF-kappaB inducing kinase (NIK) bound to Imidazobenzoxepin Compound 3

PDB DOI: https://doi.org/10.2210/pdb5T8O/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2016-09-08 Released: 2017-01-11
Deposition Author(s): Smith, M.A., McEwan, P., Hymowitz, S.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.256 (Depositor), 0.258 (DCC)
R-Value Work:
0.201 (Depositor), 0.204 (DCC)
R-Value Observed:
0.207 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Structure-Based Design of Tricyclic NF-kappa B Inducing Kinase (NIK) Inhibitors That Have High Selectivity over Phosphoinositide-3-kinase (PI3K).

Castanedo, G.M., Blaquiere, N., Beresini, M., Bravo, B., Brightbill, H., Chen, J., Cui, H.F., Eigenbrot, C., Everett, C., Feng, J., Godemann, R., Gogol, E., Hymowitz, S., Johnson, A., Kayagaki, N., Kohli, P.B., Knuppel, K., Kraemer, J., Kruger, S., Loke, P., McEwan, P., Montalbetti, C., Roberts, D.A., Smith, M., Steinbacher, S., Sujatha-Bhaskar, S., Takahashi, R., Wang, X., Wu, L.C., Zhang, Y., Staben, S.T.

(2017) J Med Chem 60: 627-640

PubMed: 28005357 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.6b01363
Primary Citation Related Structures:
5T8F, 5T8O, 5T8P, 5T8Q

PubMed Abstract:
We report here structure-guided optimization of a novel series of NF-κB inducing kinase (NIK) inhibitors. Starting from a modestly potent, low molecular weight lead, activity was improved by designing a type 11/2 binding mode that accessed a back pocket past the methionine-471 gatekeeper. Divergent binding modes in NIK and PI3K were exploited to dampen PI3K inhibition while maintaining NIK inhibition within these series. Potent compounds were discovered that selectively inhibit the nuclear translocation of NF-κB2 (p52/REL-B) but not canonical NF-κB1 (REL-A/p50).

Organizational Affiliation

Genentech, Inc. 1 DNA Way, South San Francisco, California 94080, United States.

Macromolecule Content

Total Structure Weight: 78.38 kDa
Atom Count: 5,462
Modeled Residue Count: 652
Deposited Residue Count: 698
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase kinase kinase 14	A, B	349	Mus musculus	Mutation(s): 0 Gene Names: Map3k14, Nik EC: 2.7.11.25
UniProt
Find proteins for Q9WUL6 (Mus musculus) Explore Q9WUL6 Go to UniProtKB: Q9WUL6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9WUL6
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
76Z Query on 76Z Download:Ideal Coordinates CCD File SDF format, chain K [auth B] SDF format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain G [auth A]	G [auth A], K [auth B]	10-(3-methyl-3-oxidanyl-but-1-ynyl)-5,6-dihydroimidazo[1,2-d][1,4]benzoxazepine-2-carboxamide C₁₇ H₁₇ N₃ O₃ CMHKURIYUXPNNR-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth B]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain I [auth B] SDF format, chain H [auth B] SDF format, chain F [auth A] SDF format, chain E [auth A] SDF format, chain D [auth A] SDF format, chain C [auth A] MOL2 format, chain J [auth B] MOL2 format, chain I [auth B] MOL2 format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain C [auth A] mmCIF format, chain J [auth B] mmCIF format, chain I [auth B] mmCIF format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain C [auth A]	C [auth A] D [auth A] E [auth A] F [auth A] H [auth B] C [auth A], D [auth A], E [auth A], F [auth A], H [auth B], I [auth B], J [auth B]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] 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] Interactions & Density Focus chain C [auth A] 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]