7USI

BRD2-BD1 in complex with MDP5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Targeting BRD4 and PI3K signaling pathways for the treatment of medulloblastoma.

Sethi, B.Kumar, V.Jayasinghe, T.D.Dong, Y.Ronning, D.R.Zhong, H.A.Coulter, D.W.Mahato, R.I.

(2023) J Control Release 354: 80-90

  • DOI: https://doi.org/10.1016/j.jconrel.2022.12.055
  • Primary Citation of Related Structures:  
    7USG, 7USH, 7USI, 7USJ, 7USK

  • PubMed Abstract: 

    Medulloblastoma (MB) is a malignant pediatric brain tumor which shows upregulation of MYC and sonic hedgehog (SHH) signaling. SHH inhibitors face acquired resistance, which is a major cause of relapse. Further, direct MYC oncogene inhibition is challenging, inhibition of MYC upstream insulin-like growth factor/ phosphatidylinositol-4,5-bisphosphate 3-kinase (IGF/PI3K) is a promising alternative. While PI3K inhibition activates resistance mechanisms, simultaneous inhibition of bromodomain-containing protein 4 (BRD4) and PI3K can overcome resistance. We synthesized a new molecule 8-(2,3-dihydrobenzo[b] [1, 4] dioxin-6-yl)-2-morpholino-4H-chromen-4-one (MDP5) that targets both BRD4 and PI3K pathways. We used X-ray crystal structures and a molecular modeling approach to confirm the interactions between MDP5 with bromo domains (BDs) from both BRD2 and BRD4, and molecular modeling for PI3K binding. MDP5 was shown to inhibit target pathways and MB cell growth in vitro and in vivo. MDP5 showed higher potency in DAOY cells (IC 50 5.5 μM) compared to SF2523 (IC 50 12.6 μM), and its IC 50 values in HD-MB03 cells were like SF2523. Treatment of MB cells with MDP5 significantly decreased colony formation, increased apoptosis, and halted cell cycle progression. Further, MDP5 was well tolerated in NSG mice bearing either xenograft or orthotopic MB tumors at the dose of 20 mg/kg, and significantly reduced tumor growth and prolonged animal survival.


  • Organizational Affiliation

    Department of Pharmaceutical Sciences, the University of Nebraska Medical Center, Omaha, NE 68198, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 2
A, B, C, D, E
A, B, C, D, E, F
114Homo sapiensMutation(s): 0 
Gene Names: BRD2KIAA9001RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens)
Explore P25440 
Go to UniProtKB:  P25440
PHAROS:  P25440
GTEx:  ENSG00000204256 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP25440
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O6O (Subject of Investigation/LOI)
Query on O6O

Download Ideal Coordinates CCD File 
EB [auth F]
G [auth A]
HA [auth C]
NA [auth D]
T [auth B]
EB [auth F],
G [auth A],
HA [auth C],
NA [auth D],
T [auth B],
TA [auth E]
(8M)-8-(2,3-dihydro-1,4-benzodioxin-6-yl)-2-(morpholin-4-yl)-4H-1-benzopyran-4-one
C21 H19 N O5
PZGGPBWCQBEFPX-UHFFFAOYSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
FB [auth F]TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
FA [auth C]
H [auth A]
I [auth A]
J [auth A]
L [auth A]
FA [auth C],
H [auth A],
I [auth A],
J [auth A],
L [auth A],
UA [auth E],
W [auth B]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
DMS
Query on DMS

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BA [auth B]
GA [auth C]
GB [auth F]
JA [auth C]
LA [auth C]
BA [auth B],
GA [auth C],
GB [auth F],
JA [auth C],
LA [auth C],
M [auth A],
PA [auth D],
ZA [auth E]
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
AB [auth E]
BB [auth E]
CA [auth B]
DA [auth B]
AA [auth B],
AB [auth E],
BB [auth E],
CA [auth B],
DA [auth B],
HB [auth F],
IA [auth C],
IB [auth F],
JB [auth F],
K [auth A],
KA [auth C],
N [auth A],
O [auth A],
OA [auth D],
P [auth A],
Q [auth A],
RA [auth E],
SA [auth E],
U [auth B],
V [auth B],
VA [auth E],
WA [auth E],
X [auth B],
XA [auth E],
Y [auth B],
YA [auth E],
Z [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

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CB [auth E]
EA [auth B]
KB [auth F]
MA [auth C]
QA [auth D]
CB [auth E],
EA [auth B],
KB [auth F],
MA [auth C],
QA [auth D],
R [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
DB [auth E],
S [auth A]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.250 
  • R-Value Work: 0.201 
  • R-Value Observed: 0.203 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.81α = 90
b = 149.872β = 112.27
c = 63.819γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALAdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-18
    Type: Initial release
  • Version 1.1: 2023-10-25
    Changes: Data collection, Refinement description