5EK9 | pdb_00005ek9

Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline inhibitor

• PDB DOI: https://doi.org/10.2210/pdb5EK9/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-11-03 Released: 2016-11-16 
• Deposition Author(s): Tallant, C., Slavish, P.J., Siejka, P., Bharatham, N., Shadrick, W.R., Chai, S., Young, B.M., Boyd, V.A., Heroven, C., Picaud, S., Fedorov, O., Chen, T., Lee, R.E., Guy, R.K., Shelat, A.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free: 
  0.223 (Depositor), 0.232 (DCC) 
• R-Value Work: 
  0.182 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.184 (Depositor) 

Literature

Exploiting a water network to achieve enthalpy-driven, bromodomain-selective BET inhibitors.

Shadrick, W.R., Slavish, P.J., Chai, S.C., Waddell, B., Connelly, M., Low, J.A., Tallant, C., Young, B.M., Bharatham, N., Knapp, S., Boyd, V.A., Morfouace, M., Roussel, M.F., Chen, T., Lee, R.E., Kiplin Guy, R., Shelat, A.A., Potter, P.M.

(2018) Bioorg Med Chem 26: 25-36

• PubMed: 29170024 
• DOI: https://doi.org/10.1016/j.bmc.2017.10.042
• Primary Citation Related Structures: 
  5EK9


• PubMed Abstract: 
  

  Within the last decade, the Bromodomain and Extra-Terminal domain family (BET) of proteins have emerged as promising drug targets in diverse clinical indications including oncology, auto-immune disease, heart failure, and male contraception. The BET family consists of four isoforms (BRD2, BRD3, BRD4, and BRDT/BRDT6) which are distinguished by the presence of two tandem bromodomains (BD1 and BD2) that independently recognize acetylated-lysine (KAc) residues and appear to have distinct biological roles. BET BD1 and BD2 bromodomains differ at five positions near the substrate binding pocket: the variation in the ZA channel induces different water networks nearby. We designed a set of congeneric 2- and 3-heteroaryl substituted tetrahydroquinolines (THQ) to differentially engage bound waters in the ZA channel with the goal of achieving bromodomain selectivity. SJ830599 (9) showed modest, but consistent, selectivity for BRD2-BD2. Using isothermal titration calorimetry, we showed that the binding of all THQ analogs in our study to either of the two bromodomains was enthalpy driven. Remarkably, the binding of 9 to BRD2-BD2 was marked by negative entropy and was entirely driven by enthalpy, consistent with significant restriction of conformational flexibility and/or engagement with bound waters. Co-crystallography studies confirmed that 9 did indeed stabilize a water-mediated hydrogen bond network. Finally, we report that 9 retained cytotoxicity against several pediatric cancer cell lines with EC ₅₀ values comparable to BET inhibitor (BETi) clinical candidates.

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Organizational Affiliation: 
• Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Molecular Interaction Analysis Shared Resource, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Oxford OX3 7FZ, UK; Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7DQ, UK.
Department of Tumor Cell Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA.
Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.46 kDa 
• Atom Count: 1,929 
• Modeled Residue Count: 214 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B	114	Homo sapiens	Mutation(s): 0  Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440  Go to UniProtKB:  P25440
PHAROS:  P25440 GTEx:  ENSG00000204256

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5P4	C [auth A], D [auth B]	propan-2-yl ~{N}-[(2~{S},4~{R})-1-ethanoyl-6-(furan-2-yl)-2-methyl-3,4-dihydro-2~{H}-quinolin-4-yl]carbamate C20 H24 N2 O4 OZBRAEGGHPSXJE-SUMWQHHRSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.08 Å
• R-Value Free:  0.223 (Depositor), 0.232 (DCC) 
• R-Value Work:  0.182 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.184 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 59.704	α = 90
b = 69.749	β = 90
c = 141.215	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-11-16 
Deposition Author(s): Tallant, C., Slavish, P.J., Siejka, P., Bharatham, N., Shadrick, W.R., Chai, S., Young, B.M., Boyd, V.A., Heroven, C., Picaud, S., Fedorov, O., Chen, T., Lee, R.E., Guy, R.K., Shelat, A.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2016-11-16
  Type: Initial release
  
• Version 1.1: 2017-11-29
  Changes: Database references
• Version 1.2: 2017-12-13
  Changes: Database references
• Version 1.3: 2018-01-17
  Changes: Database references
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references