[English] 日本語
Yorodumi
- PDB-9q1g: Blimp-1 with compound 5 -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9q1g
TitleBlimp-1 with compound 5
ComponentsPR domain zinc finger protein 1
KeywordsTRANSCRIPTION / factor / B-cell / lymphocyte
Function / homology
Function and homology information


regulation of extrathymic T cell differentiation / regulation of NK T cell differentiation / sebum secreting cell proliferation / morphogenesis of a branching structure / retinal bipolar neuron differentiation / regulation of natural killer cell differentiation / maternal placenta development / Specification of primordial germ cells / trophoblast giant cell differentiation / eye photoreceptor cell development ...regulation of extrathymic T cell differentiation / regulation of NK T cell differentiation / sebum secreting cell proliferation / morphogenesis of a branching structure / retinal bipolar neuron differentiation / regulation of natural killer cell differentiation / maternal placenta development / Specification of primordial germ cells / trophoblast giant cell differentiation / eye photoreceptor cell development / histone methyltransferase binding / intestinal epithelial cell development / heart valve development / coronary vasculature development / STAT3 nuclear events downstream of ALK signaling / Regulation of TP53 Expression / artery morphogenesis / aorta development / ventricular septum development / germ cell development / cell fate commitment / Transferases; Transferring one-carbon groups; Methyltransferases / post-embryonic development / methyltransferase activity / promoter-specific chromatin binding / kidney development / DNA-binding transcription repressor activity, RNA polymerase II-specific / sequence-specific double-stranded DNA binding / regulation of cell population proliferation / methylation / gene expression / adaptive immune response / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of gene expression / innate immune response / positive regulation of gene expression / regulation of transcription by RNA polymerase II / nucleolus / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus / cytoplasm
Similarity search - Function
PR domain zinc finger protein 1 / PRDM1, PR/SET domain / PR domain zinc finger protein 2, PR domain / : / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain profile. / SET domain superfamily / SET domain / Zinc finger, C2H2 type / zinc finger ...PR domain zinc finger protein 1 / PRDM1, PR/SET domain / PR domain zinc finger protein 2, PR domain / : / SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain / SET domain profile. / SET domain superfamily / SET domain / Zinc finger, C2H2 type / zinc finger / Zinc finger C2H2 type domain profile. / Zinc finger C2H2 superfamily / Zinc finger C2H2 type domain signature. / Zinc finger C2H2-type
Similarity search - Domain/homology
: / PR domain zinc finger protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.703 Å
AuthorsWatson, E.R.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: J Med Chem / Year: 2025
Title: Discovery and Characterization of Novel BLIMP-1 Heterobifunctional Ligand-Directed Degraders.
Authors: Bryan J Simmons / Lynda Groocock / Jesus Moreno / David S Peters / Meredith E Hughes / Vijay Veeravalli / Jennifer M Crawford / Matthew Chalkley / Mark Griffith / Melissa Plooster / Bo Hu / ...Authors: Bryan J Simmons / Lynda Groocock / Jesus Moreno / David S Peters / Meredith E Hughes / Vijay Veeravalli / Jennifer M Crawford / Matthew Chalkley / Mark Griffith / Melissa Plooster / Bo Hu / Jim Gamez / Jim Leisten / Michael J Barnes / Jason Chinn / Gauri Deb / Hardik Modi / Madhu Katepalli / Dahlia Weiss / Walter Won / Zhenghang Sun / Shan Yu / Cameron Reid / Andrew F Donnell / Ling Li / Edmond R Watson / Sophie Perrin-Ninkovic / Lihong Shi / Rama Krishna Narla / Christoph W Zapf / Neil Bence / Antonia Lopez-Girona / Jennifer R Riggs /
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. ...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.
History
DepositionAug 13, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 14, 2026Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PR domain zinc finger protein 1
B: PR domain zinc finger protein 1
C: PR domain zinc finger protein 1
D: PR domain zinc finger protein 1
E: PR domain zinc finger protein 1
F: PR domain zinc finger protein 1
G: PR domain zinc finger protein 1
H: PR domain zinc finger protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,70216
Polymers174,9248
Non-polymers2,7788
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)243.416, 47.866, 180.655
Angle α, β, γ (deg.)90.00, 129.18, 90.00
Int Tables number5
Space group name H-MC121

-
Components

#1: Protein
PR domain zinc finger protein 1 / BLIMP-1 / Beta-interferon gene positive regulatory domain I-binding factor / PR domain-containing ...BLIMP-1 / Beta-interferon gene positive regulatory domain I-binding factor / PR domain-containing protein 1 / Positive regulatory domain I-binding factor 1 / PRDI-BF1 / PRDI-binding factor 1


Mass: 21865.510 Da / Num. of mol.: 8 / Mutation: 37-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PRDM1, BLIMP1
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: O75626, Transferases; Transferring one-carbon groups; Methyltransferases
#2: Chemical
ChemComp-A1CNQ / (2S)-2-(4-bromophenyl)-2-(5,8-dihydropyrido[3,4-d]pyrimidin-7(6H)-yl)acetamide


Mass: 347.210 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C15H15BrN4O / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 100mM Sodium Cacodylate pH 5.5, 15% w/v PEG 6k, 0.15M Potassium Thiocyanate

-
Data collection

DiffractionMean temperature: 88 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97931 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 9, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97931 Å / Relative weight: 1
ReflectionResolution: 3.703→38.09 Å / Num. obs: 13751 / % possible obs: 77.4 % / Redundancy: 3.3 % / CC1/2: 0.991 / Net I/σ(I): 7.4
Reflection shellResolution: 3.703→3.79 Å / Mean I/σ(I) obs: 2.3 / Num. unique obs: 689 / CC1/2: 0.874

-
Processing

Software
NameVersionClassification
BUSTER2.11.8 (10-JUL-2024)refinement
XDSdata reduction
STARANISOdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.703→38.09 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.86 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.86
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2527 660 6.94 %RANDOM
Rwork0.2163 ---
obs0.2188 13751 77.4 %-
Displacement parametersBiso mean: 97.25 Å2
Baniso -1Baniso -2Baniso -3
1-9.7666 Å20 Å2-3.7205 Å2
2---14.027 Å20 Å2
3---4.2604 Å2
Refine analyzeLuzzati coordinate error obs: 0.48 Å
Refinement stepCycle: LAST / Resolution: 3.703→38.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10112 0 168 0 10280
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.00510856HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.714931HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d3493SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes1842HARMONIC5
X-RAY DIFFRACTIONt_it10544HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion1.93
X-RAY DIFFRACTIONt_other_torsion19.42
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion1373SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact7135SEMIHARMONIC4
LS refinement shellResolution: 3.703→3.74 Å
RfactorNum. reflection% reflection
Rfree0.2958 -8.87 %
Rwork0.3041 267 -
obs--63.77 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more