3P1D

Crystal structure of the bromodomain of human CREBBP in complex with N-Methyl-2-pyrrolidone (NMP)

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history. 


Literature

Histone recognition and large-scale structural analysis of the human bromodomain family.

Filippakopoulos, P., Picaud, S., Mangos, M., Keates, T., Lambert, J.P., Barsyte-Lovejoy, D., Felletar, I., Volkmer, R., Muller, S., Pawson, T., Gingras, A.C., Arrowsmith, C.H., Knapp, S.

(2012) Cell 149: 214-231

  • DOI: https://doi.org/10.1016/j.cell.2012.02.013
  • Primary Citation of Related Structures:  
    2NXB, 2OO1, 2OSS, 2OUO, 2RFJ, 3D7C, 3DAI, 3DWY, 3GG3, 3HME, 3HMF, 3HMH, 3I3J, 3IU5, 3IU6, 3LXJ, 3MB3, 3MB4, 3MQM, 3NXB, 3P1C, 3P1D, 3Q2E, 3RCW, 3TLP, 3UV2, 3UV4, 3UV5, 3UVD, 3UVW, 3UVX, 3UVY, 3UW9

  • PubMed Abstract: 

    • Bromodomains (BRDs) are protein interaction modules that specifically recognize ε-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity ...

    Bromodomains (BRDs) are protein interaction modules that specifically recognize ε-N-lysine acetylation motifs, a key event in the reading process of epigenetic marks. The 61 BRDs in the human genome cluster into eight families based on structure/sequence similarity. Here, we present 29 high-resolution crystal structures, covering all BRD families. Comprehensive crossfamily structural analysis identifies conserved and family-specific structural features that are necessary for specific acetylation-dependent substrate recognition. Screening of more than 30 representative BRDs against systematic histone-peptide arrays identifies new BRD substrates and reveals a strong influence of flanking posttranslational modifications, such as acetylation and phosphorylation, suggesting that BRDs recognize combinations of marks rather than singly acetylated sequences. We further uncovered a structural mechanism for the simultaneous binding and recognition of diverse diacetyl-containing peptides by BRD4. These data provide a foundation for structure-based drug design of specific inhibitors for this emerging target family.

    Organizational Affiliation: 

    Nuffield Department of Clinical Medicine, Structural Genomics Consortium, University of Oxford, Old Road Campus Research Building, Roosevelt Drive, Oxford OX3 7LD, UK. panagis.filippakopoulos@sgc.ox.ac.uk



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
CREB-binding protein
A, B
119Homo sapiensMutation(s): 0 
Gene Names: CREBBP, CBP
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q92793 (Homo sapiens)
Explore Q92793 
Go to UniProtKB:  Q92793
PHAROS:  Q92793
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ92793
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MB3
Query on MB3
Download Ideal Coordinates CCD File 
D [auth A],
F [auth B]		1-methylpyrrolidin-2-one
C5 H9 N O
SECXISVLQFMRJM-UHFFFAOYSA-N		 Ligand Interaction
SCN
Query on SCN
Download Ideal Coordinates CCD File 
C [auth A]THIOCYANATE ION
C N S
ZMZDMBWJUHKJPS-UHFFFAOYSA-M		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
E [auth B]POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
MB3 BindingDB:  3P1D IC50: 2.30e+6 (nM) from 1 assay(s)
PDBBind:  3P1D IC50: 2.30e+6 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.86 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.167 
  • R-Value Observed: 0.170 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 121.549α = 90
b = 121.549β = 90
c = 40.23γ = 120
Software Package:
Software NamePurpose
SCALAdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CrystalCleardata collection
MOSFLMdata reduction

Structure Validation

View Full Validation Report



View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-11-24
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2012-04-11
    Changes: Database references
  • Version 1.3: 2018-01-31
    Changes: Structure summary