7USI | pdb_00007usi

BRD2-BD1 in complex with MDP5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.250 (Depositor), 0.250 (DCC) 
  • R-Value Work: 
    0.201 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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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 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.

Macromolecule Content 

  • Total Structure Weight: 86.67 kDa 
  • Atom Count: 5,980 
  • Modeled Residue Count: 666 
  • Deposited Residue Count: 684 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  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
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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



Download:Ideal Coordinates CCD File
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



Download:Ideal Coordinates CCD File
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 (Depositor), 0.250 (DCC) 
  • R-Value Work:  0.201 (Depositor), 0.203 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
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