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- PDB-9o91: Structure of IKZF2:CRBN:Compound 5 ternary structure -

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Basic information

Entry
Database: PDB / ID: 9o91
TitleStructure of IKZF2:CRBN:Compound 5 ternary structure
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 / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / Potential therapeutics for SARS / 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 / FOURIER SYNTHESIS / Resolution: 1.86 Å
AuthorsStrickland, C.O. / Rice, C.T.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2025
Title: Overcoming CK1 alpha liability in the discovery of a series of isoIndolinone Glutarimides as selective IKZF2 molecular glue degraders.
Authors: Zhang, X. / Deng, Q. / Dhruv, H. / Tudor, M. / Nagilla, R. / Jolivette, L.J. / Rice, C.T. / Orth, P. / Behshad, E. / Strickland, C.O. / Mohammad, H.P. / Sui, Z. / Priestley, E.S.
History
DepositionApr 17, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 9, 2025Provider: repository / Type: Initial release

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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)64,73720
Polymers62,4398
Non-polymers2,29712
Water5,134285
1
A: Protein cereblon
B: Zinc finger protein Helios
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,1845
Polymers15,6102
Non-polymers5743
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)16,1845
Polymers15,6102
Non-polymers5743
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)16,1845
Polymers15,6102
Non-polymers5743
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)16,1845
Polymers15,6102
Non-polymers5743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.160, 70.180, 78.710
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protein cereblon


Mass: 12309.062 Da / Num. of mol.: 4 / Fragment: CULT domain
Source method: isolated from a genetically manipulated source
Details: CRBN with 4 mutations to help crystallization: C318S, C322S, C343S, C366S
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 / Fragment: zinc finger domain 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IKZF2, HELIOS, ZNFN1A2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9UKS7
#3: Chemical
ChemComp-A1CAC / (3S)-3-[(5M)-1-oxo-5-{4-[(pyrrolidin-1-yl)methyl]-1H-pyrrolo[2,3-b]pyridin-6-yl}-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione


Mass: 443.498 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H25N5O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.04 Å3/Da / Density % sol: 39.76 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Magnesium chloride 0.1 M TRIS pH 8.5 33 % w/v PEG 4000

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Data collection

DiffractionMean temperature: 90 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 1.03321 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Aug 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03321 Å / Relative weight: 1
ReflectionResolution: 1.86→46.2 Å / Num. obs: 41050 / % possible obs: 98.7 % / Redundancy: 6.8 % / CC1/2: 0.992 / Rmerge(I) obs: 0.3 / Rpim(I) all: 0.123 / Rrim(I) all: 0.325 / Χ2: 1.02 / Net I/σ(I): 8.9
Reflection shellResolution: 1.87→1.91 Å / % possible obs: 94.1 % / Redundancy: 5.6 % / Rmerge(I) obs: 0.91 / Num. measured all: 13878 / Num. unique obs: 2493 / CC1/2: 0.839 / Rpim(I) all: 0.412 / Rrim(I) all: 1.002 / Χ2: 0.96 / Net I/σ(I) obs: 3.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
Aimlessdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.86→46.2 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.487 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21758 2032 4.9 %RANDOM
Rwork0.17525 ---
obs0.17734 39620 98.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.661 Å2
Baniso -1Baniso -2Baniso -3
1--0.38 Å2-0 Å2-0.4 Å2
2--2.84 Å20 Å2
3----2.45 Å2
Refinement stepCycle: 1 / Resolution: 1.86→46.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4258 0 140 285 4683
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0124532
X-RAY DIFFRACTIONr_bond_other_d0.0010.0164129
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.8056168
X-RAY DIFFRACTIONr_angle_other_deg0.5211.7489560
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.5745537
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.272534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07710721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0750.2663
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025187
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021033
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.8581.8872172
X-RAY DIFFRACTIONr_mcbond_other1.8561.8872172
X-RAY DIFFRACTIONr_mcangle_it2.9363.3622701
X-RAY DIFFRACTIONr_mcangle_other2.9383.3642702
X-RAY DIFFRACTIONr_scbond_it2.6012.1382360
X-RAY DIFFRACTIONr_scbond_other2.6012.1392361
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.1483.7773468
X-RAY DIFFRACTIONr_long_range_B_refined5.86324.015046
X-RAY DIFFRACTIONr_long_range_B_other5.83523.165001
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.86→1.908 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 127 -
Rwork0.262 2750 -
obs--92.27 %

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