5MPN | pdb_00005mpn

Crystal structure of CREBBP bromodomain complexed with FA26

• PDB DOI: https://doi.org/10.2210/pdb5MPN/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-12-16 Released: 2018-01-17 
• Deposition Author(s): Zhu, J., Caflisch, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free: 
  0.167 (Depositor), 0.169 (DCC) 
• R-Value Work: 
  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Literature

Binding Motifs in the CBP Bromodomain: An Analysis of 20 Crystal Structures of Complexes with Small Molecules.

Zhu, J., Dong, J., Batiste, L., Unzue, A., Dolbois, A., Pascanu, V., Sledz, P., Nevado, C., Caflisch, A.

(2018) ACS Med Chem Lett 9: 929-934

• PubMed: 30258543 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00286
• Primary Citation Related Structures: 
  5EIC, 5ENG, 5EP7, 5H85, 5MME, 5MMG, 5MPK, 5MPN, 5OWK, 6FQO, 6FQU, 6FR0, 6FRF


• PubMed Abstract: 
  

  We analyze 20 crystal structures of complexes between the CBP bromodomain and small-molecule ligands that belong to eight different chemotypes identified by docking. The binding motif of the moiety that mimics the natural ligand (acetylated side chain of lysine) at the bottom of the binding pocket is conserved. In stark contrast, the rest of the ligands form different interactions with different side chains and backbone polar groups on the outer rim of the binding pocket. Hydrogen bonds are direct or water-bridged. van der Waals contacts are optimized by rotations of hydrophobic side chains and a slight inward displacement of the ZA loop. Rare types of interactions are observed for some of the ligands.

---

Organizational Affiliation: 
• Department of Biochemistry, and Department of Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 14.96 kDa 
• Atom Count: 1,273 
• Modeled Residue Count: 118 
• Deposited Residue Count: 119 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A	119	Homo sapiens	Mutation(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 GTEx:  ENSG00000005339

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YE5	B [auth A], C [auth A]	1-[4-ethoxy-3-[3-(2~{H}-1,2,3,4-tetrazol-5-yl)phenyl]phenyl]ethanone C17 H16 N4 O2 XRDCFDYQIVETFM-UHFFFAOYSA-N
EDO	D [auth A], E [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.23 Å
• R-Value Free:  0.167 (Depositor), 0.169 (DCC) 
• R-Value Work:  0.158 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.584	α = 90
b = 44.723	β = 90
c = 60.757	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-01-17 
Deposition Author(s): Zhu, J., Caflisch, A.

Revision History  

• Version 1.0: 2018-01-17
  Type: Initial release
  
• Version 1.1: 2018-08-29
  Changes: Data collection, Database references
• Version 1.2: 2018-10-10
  Changes: Data collection, Database references
• Version 1.3: 2019-10-16
  Changes: Data collection
• Version 1.4: 2024-05-08
  Changes: Data collection, Database references