4TZU

Crystal Structure of Murine Cereblon in Complex with Pomalidomide

PDB DOI: https://doi.org/10.2210/pdb4TZU/pdb

Classification: LIGASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-10 Released: 2014-08-06
Deposition Author(s): Chamberlain, P.P., Pagarigan, B., Delker, S., Leon, B.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.239
R-Value Work: 0.196
R-Value Observed: 0.198

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Literature

Structural Basis for Responsiveness to Thalidomide-Analog Drugs Defined by the Crystal Structure of the Human Cereblon:DDB1:Lenalidomide Complex

Chamberlain, P.P., Wang, M., Riley, M., Delker, S., Ito, T., Hideki, A., Mori, T., Handa, H., Hakoshima, T., Daniel, T.O., Cathers, B.E., Lopez-Girona, A., Miller, K., Carmel, G., Pagarigan, B., Leon, B., Rychak, E., Corral, L., Ren, Y.

To be published.

Macromolecule Content

Total Structure Weight: 50.46 kDa
Atom Count: 3,162
Modelled Residue Count: 361
Deposited Residue Count: 432
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein cereblon	A, B, C, D	108	Mus musculus	Mutation(s): 0 Gene Names: Crbn
UniProt & NIH Common Fund Data Resources
Find proteins for Q8C7D2 (Mus musculus) Explore Q8C7D2 Go to UniProtKB: Q8C7D2
IMPC: MGI:1913277
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q8C7D2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
Y70 Query on Y70 Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain Q [auth C] SDF format, chain H [auth A] SDF format, chain T [auth D] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] MOL2 format, chain H [auth A] MOL2 format, chain T [auth D]	H [auth A], M [auth B], Q [auth C], T [auth D]	S-Pomalidomide C₁₃ H₁₁ N₃ O₄ UVSMNLNDYGZFPF-QMMMGPOBSA-N		Interactions Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D] Interactions & Density Focus chain H [auth A] Focus chain M [auth B] Focus chain Q [auth C] Focus chain T [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain O [auth C] SDF format, chain R [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] MOL2 format, chain R [auth D]	E [auth A] F [auth A] I [auth B] J [auth B] K [auth B] E [auth A], F [auth A], I [auth B], J [auth B], K [auth B], N [auth C], O [auth C], R [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain N [auth C] Focus chain O [auth C] Focus chain R [auth D]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain S [auth D] SDF format, chain G [auth A] SDF format, chain L [auth B] SDF format, chain P [auth C] MOL2 format, chain S [auth D] MOL2 format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain P [auth C]	G [auth A], L [auth B], P [auth C], S [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D] Interactions & Density Focus chain G [auth A] Focus chain L [auth B] Focus chain P [auth C] Focus chain S [auth D]

Binding Affinity Annotations
ID	Source	Binding Affinity
Y70	BindingDB: 4TZU	Ki: 1.00e+4 (nM) from 1 assay(s)
Y70	BindingDB: 4TZU	IC50: min: 63.1, max: 2.58e+4 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.239
R-Value Work: 0.196
R-Value Observed: 0.198
Space Group: I 2 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 143.34	α = 90
b = 143.34	β = 90
c = 143.34	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-08-06

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-08-06
Type: Initial release
Version 2.0: 2017-09-27
Changes: Atomic model, Database references, Derived calculations, Other, Refinement description, Source and taxonomy
Version 2.1: 2023-12-27
Changes: Data collection, Database references, Refinement description

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Help and Resources

4TZU

Crystal Structure of Murine Cereblon in Complex with Pomalidomide

Structural Basis for Responsiveness to Thalidomide-Analog Drugs Defined by the Crystal Structure of the Human Cereblon:DDB1:Lenalidomide Complex

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)