7M40 | pdb_00007m40

Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4)

• PDB DOI: https://doi.org/10.2210/pdb7M40/pdb

• Classification: GENE REGULATION
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 


• Deposited: 2021-03-19 Released: 2021-05-12 
• Deposition Author(s): Perveen, S., Dong, A., Tempel, W., Zepeda-Velazquez, C., Abbey, M., McLeod, D., Marcellus, R., Mohammed, M., Ensan, D., Panagopoulos, D., Trush, V., Gibson, E., Brown, P.J., Arrowsmith, C.H., Schapira, M., Al-awar, R., Vedadi, M., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free: 
  0.236 (Depositor), 0.249 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Starting Model: experimental

Literature

Discovery of small molecule antagonists of human Retinoblastoma Binding Protein 4 (RBBP4)

Perveen, S., Zepeda-Velazquez, C., Abbey, M., McLeod, D., Marcellus, R., Mohammed, M., Ensan, D., Panagopoulos, D., Trush, V., Gibson, E., Tempel, W., Brown, P.J., Arrowsmith, C.H., Schapira, M., Al-awar, R., Vedadi, M., Structural Genomics Consortium (SGC)

To be published.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 100.62 kDa 
• Atom Count: 6,444 
• Modeled Residue Count: 780 
• Deposited Residue Count: 886 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone-binding protein RBBP4	A, B	443	Homo sapiens	Mutation(s): 0  Gene Names: RBBP4, RBAP48
UniProt & NIH Common Fund Data Resources
Find proteins for Q09028 (Homo sapiens) Explore Q09028  Go to UniProtKB:  Q09028
PHAROS:  Q09028 GTEx:  ENSG00000162521

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YQJ (Subject of Investigation/LOI)	C [auth A], D [auth B]	N~3~-{4-[3-(dimethylamino)pyrrolidin-1-yl]-6,7-dimethoxyquinazolin-2-yl}-N~1~,N~1~-dimethylpropane-1,3-diamine C21 H34 N6 O2 YLRHAJMWBVABHS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.88 Å
• R-Value Free:  0.236 (Depositor), 0.249 (DCC) 
• R-Value Work:  0.184 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Diffraction Data: https://doi.org/10.18430/M37M40

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 75.82	α = 90
b = 59.857	β = 93.73
c = 102.011	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PHASER	phasing
PDB_EXTRACT	data extraction
HKL-3000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-05-12 
Deposition Author(s): Perveen, S., Dong, A., Tempel, W., Zepeda-Velazquez, C., Abbey, M., McLeod, D., Marcellus, R., Mohammed, M., Ensan, D., Panagopoulos, D., Trush, V., Gibson, E., Brown, P.J., Arrowsmith, C.H., Schapira, M., Al-awar, R., Vedadi, M., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2021-05-12
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Data collection, Database references, Refinement description