7Q5O

Bromodomain-containing 2 BD2 in complex with the inhibitor CRCM5484


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 

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

CRCM5484: A BET-BDII Selective Compound with Differential Anti-leukemic Drug Modulation

Carrasco, K.Montersino, C.Derviaux, C.Saez-Ayala, M.Hoffer, L.Restouin, A.Castellano, R.Casassa, J.Roche, P.Pasquier, E.Combes, S.Morelli, X.Collette, Y.Betzi, S.

(2022) J Med Chem 65: 5660-5674


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Bromodomain-containing protein 2110Homo 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 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
8M6 (Subject of Investigation/LOI)
Query on 8M6

Download Ideal Coordinates CCD File 
B [auth A]2-[[11-ethanoyl-4-(furan-2-ylmethyl)-3-oxidanylidene-8-thia-4,6,11-triazatricyclo[7.4.0.0^{2,7}]trideca-1(9),2(7),5-trien-5-yl]sulfanyl]-~{N}-(2-methylpyridin-3-yl)ethanamide
C24 H23 N5 O4 S2
PQYXGDZAWKQEEM-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
8M6 BindingDB:  7Q5O IC50: min: 71, max: 4700 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.246 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.218 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.43α = 90
b = 72.494β = 90
c = 32.041γ = 90
Software Package:
Software NamePurpose
xia2data scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
xia2data reduction
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: 2022-04-20
    Type: Initial release
  • Version 1.1: 2024-01-31
    Changes: Data collection, Refinement description