7XNG | pdb_00007xng

Crystal structure of CBP bromodomain liganded with Y08092(31g)

• PDB DOI: https://doi.org/10.2210/pdb7XNG/pdb

• Classification: TRANSFERASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2022-04-28 Released: 2022-06-01 
• Deposition Author(s): Xiang, Q., Zhang, Y., Wang, C., Song, M., Xu, Y.
• Funding Organization(s): National Natural Science Foundation of China (NSFC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free: 
  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 
  0.194 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of CBP bromodomain liganded with Y08092(31g)

Xiang, Q., Zhang, Y., Wang, C., Song, M., Xu, Y.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 32.85 kDa 
• Atom Count: 2,023 
• Modeled Residue Count: 226 
• Deposited Residue Count: 266 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A, B	133	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GI5 (Subject of Investigation/LOI)	C [auth A], F [auth B]	3-[(1-ethanoylindol-3-yl)carbonylamino]-5-[[(2S)-oxan-2-yl]oxymethyl]benzoic acid C24 H24 N2 O6 MBYTWRXIPXJQJP-QFIPXVFZSA-N
PEG	E [auth B]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
GOL	D [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GI5	BindingDB:  7XNG	IC50: min: 1000, max: 2510 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.35 Å
• R-Value Free:  0.242 (Depositor), 0.250 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.200 (DCC) 
• R-Value Observed: 0.194 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.119	α = 90
b = 75.309	β = 90
c = 123.489	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
iMOSFLM	data reduction
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2022-06-01 
Deposition Author(s): Xiang, Q., Zhang, Y., Wang, C., Song, M., Xu, Y.

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Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	--

Revision History  

• Version 1.0: 2022-06-01
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description