9Q1G | pdb_00009q1g

Blimp-1 with compound 5

PDB DOI: https://doi.org/10.2210/pdb9Q1G/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2025-08-13 Released: 2026-01-14
Deposition Author(s): Watson, E.R.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.70 Å
R-Value Free:
0.253 (Depositor), 0.234 (DCC)
R-Value Work:
0.216 (Depositor), 0.224 (DCC)
R-Value Observed:
0.219 (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

Discovery and Characterization of Novel BLIMP-1 Heterobifunctional Ligand-Directed Degraders.

Simmons, B.J., Groocock, L., Moreno, J., Peters, D.S., Hughes, M.E., Veeravalli, V., Crawford, J.M., Chalkley, M., Griffith, M., Plooster, M., Hu, B., Gamez, J., Leisten, J., Barnes, M.J., Chinn, J., Deb, G., Modi, H., Katepalli, M., Weiss, D., Won, W., Sun, Z., Yu, S., Reid, C., Donnell, A.F., Li, L., Watson, E.R., Perrin-Ninkovic, S., Shi, L., Narla, R.K., Zapf, C.W., Bence, N., Lopez-Girona, A., Riggs, J.R.

(2025) J Med Chem 68: 25385-25402

PubMed: 41284831 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c02363
Primary Citation Related Structures:
9Q1G, 9Q33

PubMed Abstract:
B-lymphocyte-induced maturation protein 1 (BLIMP-1/PRDM1) is a master transcriptional repressor essential for terminal differentiation of activated B-cells into bone-marrow resident plasma cells. Multiple myeloma (MM) is a plasma cell malignancy wherein the BLIMP-1 regulon remains critical to support basal cell functions, such as an elevated metabolic state and immunoglobulin production that underlie disease manifestation and tumor cell proliferation. It is predicted that perturbation of BLIMP-1 will significantly impact tumor cell homeostasis and ultimately reduce MM cell survival. Herein, we describe the discovery and optimization of the first orally bioavailable BLIMP-1 heterobifunctional ligand-directed degrader (LDD) and demonstration of the expected antitumor response and immunomodulatory biology following BLIMP-1 degradation using preclinical in vivo MM models.

Organizational Affiliation

Bristol Myers Squibb, 10300 Campus Point Dr. Suite 100, San Diego, California 92121, United States.

Macromolecule Content

Total Structure Weight: 177.7 kDa
Atom Count: 10,392
Modeled Residue Count: 1,253
Deposited Residue Count: 1,504
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PR domain zinc finger protein 1	A, B, C, D, E A, B, C, D, E, F, G, H	188	Homo sapiens	Mutation(s): 0 Gene Names: PRDM1, BLIMP1 EC: 2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O75626 (Homo sapiens) Explore O75626 Go to UniProtKB: O75626
PHAROS: O75626 GTEx: ENSG00000057657
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O75626
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1CNQ (Subject of Investigation/LOI) Query on A1CNQ Download:Ideal Coordinates CCD File SDF format, chain P [auth H] SDF format, chain O [auth G] SDF format, chain N [auth F] SDF format, chain M [auth E] SDF format, chain L [auth D] SDF format, chain K [auth C] SDF format, chain J [auth B] SDF format, chain I [auth A] MOL2 format, chain P [auth H] MOL2 format, chain O [auth G] MOL2 format, chain N [auth F] MOL2 format, chain M [auth E] MOL2 format, chain L [auth D] MOL2 format, chain K [auth C] MOL2 format, chain J [auth B] MOL2 format, chain I [auth A] mmCIF format, chain P [auth H] mmCIF format, chain O [auth G] mmCIF format, chain N [auth F] mmCIF format, chain M [auth E] mmCIF format, chain L [auth D] mmCIF format, chain K [auth C] mmCIF format, chain J [auth B] mmCIF format, chain I [auth A]	I [auth A] J [auth B] K [auth C] L [auth D] M [auth E] I [auth A], J [auth B], K [auth C], L [auth D], M [auth E], N [auth F], O [auth G], P [auth H]	(2S)-2-(4-bromophenyl)-2-(5,8-dihydropyrido[3,4-d]pyrimidin-7(6H)-yl)acetamide C₁₅ H₁₅ Br N₄ O HVNREMAUPHVTGZ-AWEZNQCLSA-N		Interactions Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H] Interactions & Density Focus chain I [auth A] Focus chain J [auth B] Focus chain K [auth C] Focus chain L [auth D] Focus chain M [auth E] Focus chain N [auth F] Focus chain O [auth G] Focus chain P [auth H]