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- PDB-9ohr: Structure of CRBN:IKZF2:Compound 35 -

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Basic information

Entry
Database: PDB / ID: 9ohr
TitleStructure of CRBN:IKZF2:Compound 35
Components
  • Protein cereblon
  • Zinc finger protein Helios
KeywordsIMMUNE SYSTEM / Protein Degrader
Function / homology
Function and homology information


negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination ...negative regulation of monoatomic ion transmembrane transport / Cul4A-RING E3 ubiquitin ligase complex / locomotory exploration behavior / positive regulation of Wnt signaling pathway / negative regulation of protein-containing complex assembly / positive regulation of protein-containing complex assembly / Potential therapeutics for SARS / proteasome-mediated ubiquitin-dependent protein catabolic process / transmembrane transporter binding / protein ubiquitination / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / perinuclear region of cytoplasm / zinc ion binding / metal ion binding / nucleus / membrane / cytosol / cytoplasm
Similarity search - Function
: / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) ...: / Yippee/Mis18/Cereblon / Yippee zinc-binding/DNA-binding /Mis18, centromere assembly / CULT domain / CULT domain profile. / Lon N-terminal domain profile. / Lon protease, N-terminal domain / Lon protease, N-terminal domain superfamily / ATP-dependent protease La (LON) substrate-binding domain / Found in ATP-dependent protease La (LON) / PUA-like superfamily / 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
: / Protein cereblon / Zinc finger protein Helios
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å
AuthorsStrickland, C.O. / Rice, C.T.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery of a Novel Series of iso -Indolinone-Based Glutarimides as Highly Efficacious and Selective IKZF2 Molecular Glue Degraders.
Authors: Zhang, X. / Dhruv, H. / Deng, Q. / Tudor, M. / Bechtel, N. / Nagilla, R. / Jolivette, L. / Rice, C.T. / Orth, P. / Behshad, E. / Strickland, C. / Mohammad, H.P. / Bai, L. / McEachern, D. / ...Authors: Zhang, X. / Dhruv, H. / Deng, Q. / Tudor, M. / Bechtel, N. / Nagilla, R. / Jolivette, L. / Rice, C.T. / Orth, P. / Behshad, E. / Strickland, C. / Mohammad, H.P. / Bai, L. / McEachern, D. / Wang, S. / Sui, Z. / Priestley, E.S.
History
DepositionMay 5, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 24, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein cereblon
B: Zinc finger protein Helios
C: Protein cereblon
D: Zinc finger protein Helios
E: Protein cereblon
F: Zinc finger protein Helios
G: Protein cereblon
H: Zinc finger protein Helios
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,02621
Polymers62,4398
Non-polymers2,58713
Water66737
1
A: Protein cereblon
B: Zinc finger protein Helios
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2405
Polymers15,6102
Non-polymers6303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Protein cereblon
D: Zinc finger protein Helios
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2405
Polymers15,6102
Non-polymers6303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
E: Protein cereblon
F: Zinc finger protein Helios
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2405
Polymers15,6102
Non-polymers6303
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
G: Protein cereblon
H: Zinc finger protein Helios
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,3066
Polymers15,6102
Non-polymers6964
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.463, 45.270, 65.493
Angle α, β, γ (deg.)99.92, 90.58, 104.38
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Protein cereblon


Mass: 12309.062 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: IKZF2 ZF2 Domain / Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SW2
#2: Protein/peptide
Zinc finger protein Helios / Ikaros family zinc finger protein 2


Mass: 3300.756 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: Cereblon TBD / Source: (gene. exp.) Homo sapiens (human) / Gene: IKZF2, HELIOS, ZNFN1A2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKS7
#3: Chemical
ChemComp-A1CBG / (3S)-3-[(5M)-5-{1-(oxetan-3-yl)-4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione


Mass: 499.561 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H29N5O4 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

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

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.85 %
Crystal growTemperature: 291 K / Method: vapor diffusion
Details: 0.2 M Magnesium Chloride, 0.5 M Sodium Chloride, 0.1 M Tris-HCl pH 8.1, 32.5% w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.97628 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 21, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97628 Å / Relative weight: 1
ReflectionResolution: 2.34→29.68 Å / Num. obs: 19467 / % possible obs: 94.8 % / Redundancy: 3.2 % / CC1/2: 0.908 / Rmerge(I) obs: 0.182 / Rpim(I) all: 0.13 / Rrim(I) all: 0.225 / Χ2: 0.84 / Net I/σ(I): 5.7 / Num. measured all: 62811
Reflection shellResolution: 2.34→2.42 Å / % possible obs: 97 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.571 / Num. measured all: 6559 / Num. unique obs: 1951 / CC1/2: 0.503 / Rpim(I) all: 0.377 / Rrim(I) all: 0.687 / Χ2: 0.53 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→29.68 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.868 / SU B: 12.096 / SU ML: 0.28 / Cross valid method: THROUGHOUT / ESU R: 1.2 / ESU R Free: 0.343 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.28975 992 5.1 %RANDOM
Rwork0.2244 ---
obs0.22768 18455 94.74 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 37.426 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å2-0 Å2-0.01 Å2
2---0.02 Å2-0.08 Å2
3---0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.34→29.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4211 0 157 37 4405
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124503
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164040
X-RAY DIFFRACTIONr_angle_refined_deg1.5021.8036144
X-RAY DIFFRACTIONr_angle_other_deg0.5441.7429364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8235538
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.99527
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025123
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02993
X-RAY DIFFRACTIONr_mcbond_it3.5353.832176
X-RAY DIFFRACTIONr_mcbond_other3.5343.832176
X-RAY DIFFRACTIONr_mcangle_it5.5846.842706
X-RAY DIFFRACTIONr_mcangle_other5.5836.8412707
X-RAY DIFFRACTIONr_scbond_it3.1993.9432327
X-RAY DIFFRACTIONr_scbond_other3.1993.9442328
X-RAY DIFFRACTIONr_scangle_other4.9867.1533431
X-RAY DIFFRACTIONr_long_range_B_refined8.28244.615031
X-RAY DIFFRACTIONr_long_range_B_other8.28244.615032
LS refinement shellResolution: 2.34→2.4 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 77 -
Rwork0.288 1384 -
obs--96.31 %

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