7C3Y

Crystal structure of the N-terminal domain of human MdmX protein in complex with Nutlin3a

• PDB DOI: https://doi.org/10.2210/pdb7C3Y/pdb

• Classification: ONCOPROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2020-05-14 Released: 2020-06-17 
• Deposition Author(s): Su, Z.D., Cheng, X.Y., Zhang, B.L., Kuang, Z.K., Yang, J., Li, Z.C., Yu, J.P., Zhao, Z.T., Cao, C.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.227 
• R-Value Work: 0.200 

Starting Models: experimental

Literature

Crystal structure of the N-terminal domain of human MdmX protein in complex with Nutlin3a

Su, Z.D., Cheng, X.Y., Zhang, B.L., Kuang, Z.K., Yang, J., Li, Z.C., Yu, J.P., Cao, C.Z., Zhao, Z.T.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 11.89 kDa 
• Atom Count: 856 
• Modelled Residue Count: 96 
• Deposited Residue Count: 96 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protein Mdm4	A	96	Homo sapiens	Mutation(s): 0  Gene Names: MDM4, MDMX
UniProt & NIH Common Fund Data Resources
Find proteins for O15151 (Homo sapiens) Explore O15151  Go to UniProtKB:  O15151
PHAROS:  O15151 GTEx:  ENSG00000198625

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NUT (Subject of Investigation/LOI)	C [auth A]	4-({(4S,5R)-4,5-bis(4-chlorophenyl)-2-[4-methoxy-2-(propan-2-yloxy)phenyl]-4,5-dihydro-1H-imidazol-1-yl}carbonyl)piperazin-2-one C30 H30 Cl2 N4 O4 BDUHCSBCVGXTJM-WUFINQPMSA-N
O4B	B [auth A]	1,4,7,10,13,16-HEXAOXACYCLOOCTADECANE C12 H24 O6 XEZNGIUYQVAUSS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
NUT	BindingDB:  7C3Y	Ki: min: 1599, max: 6.90e+4 (nM) from 2 assay(s)
		IC50: min: 4300, max: 1.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.63 Å
• R-Value Free: 0.227 
• R-Value Work: 0.200 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.552	α = 90
b = 47.552	β = 90
c = 90.676	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-17 
Deposition Author(s): Su, Z.D., Cheng, X.Y., Zhang, B.L., Kuang, Z.K., Yang, J., Li, Z.C., Yu, J.P., Zhao, Z.T., Cao, C.Z.

Revision History  

• Version 1.0: 2020-06-17
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Database references, Derived calculations, Refinement description