7XI0 | pdb_00007xi0

Crystal structure of CBP bromodomain liganded with CCS150

PDB DOI: https://doi.org/10.2210/pdb7XI0/pdb

Classification: PROTEIN BINDING
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-04-11 Released: 2022-07-27
Deposition Author(s): Xu, H., Xiang, Q., Wang, C., Zhang, C., Luo, G., Wu, X., Zhang, Y., Xu, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.224 (Depositor), 0.231 (DCC)
R-Value Work:
0.192 (Depositor), 0.201 (DCC)
R-Value Observed:
0.194 (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

Structural insights revealed by the cocrystal structure of CCS1477 in complex with CBP bromodomain

Xu, H., Luo, G., Wu, T., Hu, J., Wang, C., Wu, X., Zhang, Y., Xu, Y., Xiang, Q.

(2022) Biochem Biophys Res Commun 623: 17-22

DOI: https://doi.org/10.1016/j.bbrc.2022.07.021

Macromolecule Content

Total Structure Weight: 33.07 kDa
Atom Count: 2,130
Modeled Residue Count: 226
Deposited Residue Count: 266
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q92793
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EL0 (Subject of Investigation/LOI) Query on EL0 Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain E [auth B] MOL2 format, chain C [auth A] MOL2 format, chain E [auth B] mmCIF format, chain C [auth A] mmCIF format, chain E [auth B]	C [auth A], E [auth B]	(6S)-1-(3-chloranyl-4-methoxy-phenyl)-6-[5-(3,5-dimethyl-1,2-oxazol-4-yl)-1-[(3R)-1-methylsulfonylpyrrolidin-3-yl]benzimidazol-2-yl]piperidin-2-one C₂₉ H₃₂ Cl N₅ O₅ S WMRFYICILGNXCX-BWKNWUBXSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.224 (Depositor), 0.231 (DCC)
R-Value Work: 0.192 (Depositor), 0.201 (DCC)
R-Value Observed: 0.194 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.54	α = 90
b = 33.84	β = 94.65
c = 78.699	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2022-07-27

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China (NSFC)	China	22007088

Revision History (Full details and data files)

Version 1.0: 2022-07-27
Type: Initial release
Version 1.1: 2023-11-29
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.