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- PDB-9odr: Structure of CRBN TBD bound to compound C1 -

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Basic information

Entry
Database: PDB / ID: 9odr
TitleStructure of CRBN TBD bound to compound C1
ComponentsProtein cereblon
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 / perinuclear region of cytoplasm / 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) / PUA-like superfamily
Similarity search - Domain/homology
: / Protein cereblon
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsStrickland, C. / Rice, C.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2025
Title: Discovery and Characterization of PVTX-321 as a Potent and Orally Bioavailable Estrogen Receptor Degrader for ER+/HER2- Breast Cancer.
Authors: Xu, G. / Havens, C.G. / Deng, Q. / Lowenstein, C. / Samanta, D. / Vidal, B. / Behshad, E. / Russell, M. / Orth, P. / Rice, C.T. / Nagilla, R. / Kirchhoff, P. / Chen, Z. / Rej, R.K. / ...Authors: Xu, G. / Havens, C.G. / Deng, Q. / Lowenstein, C. / Samanta, D. / Vidal, B. / Behshad, E. / Russell, M. / Orth, P. / Rice, C.T. / Nagilla, R. / Kirchhoff, P. / Chen, Z. / Rej, R.K. / Acharyya, R.K. / Wu, D. / Wang, S. / Zhang, W. / Wu, W. / Jolivette, L. / Strickland, C. / Sui, Z. / Mohammad, H.P. / Zhang, X. / Priestley, E.S.
History
DepositionApr 27, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 28, 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: Protein cereblon
C: Protein cereblon
D: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,91912
Polymers49,2364
Non-polymers1,6838
Water82946
1
A: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7303
Polymers12,3091
Non-polymers4212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7303
Polymers12,3091
Non-polymers4212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7303
Polymers12,3091
Non-polymers4212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein cereblon
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7303
Polymers12,3091
Non-polymers4212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.350, 87.610, 89.500
Angle α, β, γ (deg.)90.00, 113.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein cereblon


Mass: 12309.062 Da / Num. of mol.: 4 / Fragment: TBD domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CRBN, AD-006 / Production host: Escherichia coli (E. coli) / References: UniProt: Q96SW2
#2: Chemical
ChemComp-A1CAV / (3S)-3-(6-oxo-6,8-dihydro-2H,7H-spiro[furo[2,3-e]isoindole-3,4'-piperidin]-7-yl)piperidine-2,6-dione


Mass: 355.388 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C19H21N3O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / 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: 3.29 Å3/Da / Density % sol: 62.58 %
Crystal growTemperature: 277 K / Method: evaporation / Details: 0.2M tri-Sodium citrate 18 % w/v PEG 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95373 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 21, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95373 Å / Relative weight: 1
ReflectionResolution: 2.42→46.84 Å / Num. obs: 20893 / % possible obs: 89.9 % / Redundancy: 6.9 % / CC1/2: 0.999 / Net I/σ(I): 16.2
Reflection shellResolution: 2.42→2.5 Å / Num. unique obs: 7228 / CC1/2: 0.681

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Processing

Software
NameVersionClassification
REFMAC5.8.0430refinement
XDSdata scaling
XDSdata reduction
PDB_EXTRACTdata extraction
FFTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.42→43.84 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.941 / SU B: 8.076 / SU ML: 0.181 / Cross valid method: THROUGHOUT / ESU R: 0.337 / ESU R Free: 0.239 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22761 1098 5 %RANDOM
Rwork0.18261 ---
obs0.18506 20893 89.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.179 Å2
Baniso -1Baniso -2Baniso -3
1--0.17 Å20 Å20.13 Å2
2--0.1 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: 1 / Resolution: 2.42→43.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3383 0 108 46 3537
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0123603
X-RAY DIFFRACTIONr_bond_other_d0.0010.0163280
X-RAY DIFFRACTIONr_angle_refined_deg1.7181.8074924
X-RAY DIFFRACTIONr_angle_other_deg0.5951.7387616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9115429
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.14158
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.80510571
X-RAY DIFFRACTIONr_chiral_restr0.0880.2534
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.024107
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02789
X-RAY DIFFRACTIONr_mcbond_it5.1545.4521728
X-RAY DIFFRACTIONr_mcbond_other5.1545.4521728
X-RAY DIFFRACTIONr_mcangle_it7.4259.7822153
X-RAY DIFFRACTIONr_mcangle_other7.4239.7832154
X-RAY DIFFRACTIONr_scbond_it6.1555.8931875
X-RAY DIFFRACTIONr_scbond_other6.1535.8921876
X-RAY DIFFRACTIONr_scangle_other9.02210.5552772
X-RAY DIFFRACTIONr_long_range_B_refined11.64552.013888
X-RAY DIFFRACTIONr_long_range_B_other11.64652.013887
LS refinement shellResolution: 2.42→2.481 Å
RfactorNum. reflection% reflection
Rfree0.382 29 -
Rwork0.312 830 -
obs--48.29 %

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