7XM7

Crystal Structure of the CBP in complex with the Y08188

PDB DOI: https://doi.org/10.2210/pdb7XM7/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21
Mutation(s): No

Deposited: 2022-04-25 Released: 2022-06-22
Deposition Author(s): Xiang, Q., Zhang, Y., Wang, C., Song, M., Xu, Y.
Funding Organization(s): National Natural Science Foundation of China (NSFC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.36 Å
R-Value Free: 0.257
R-Value Work: 0.208
R-Value Observed: 0.210

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

Discovery and optimization of 1-(1H-indol-1-yl)ethanone derivatives as potent and selective CBP bromodomain inhibitors

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

To be published.

Macromolecule Content

Total Structure Weight: 64.9 kDa
Atom Count: 3,971
Modelled Residue Count: 453
Deposited Residue Count: 532
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A, B, C, D	133	Homo sapiens	Mutation(s): 0 Gene Names: 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q92793
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GAY (Subject of Investigation/LOI) Query on GAY Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain G [auth B] MOL2 format, chain E [auth A] MOL2 format, chain G [auth B] mmCIF format, chain E [auth A] mmCIF format, chain G [auth B]	E [auth A], G [auth B]	3-ethanoyl-~{N}-[2-fluoranyl-3-(1-methylpyrazol-4-yl)phenyl]-7-methoxy-indolizine-1-carboxamide C₂₂ H₁₉ F N₄ O₃ KERKYEVISFXSSG-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain G [auth B] Interactions & Density Focus chain E [auth A] Focus chain G [auth B]
PEG Query on PEG Download Ideal Coordinates CCD File SDF format, chain J [auth C] MOL2 format, chain J [auth C] mmCIF format, chain J [auth C]	J [auth C]	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Interactions & Density Focus chain J [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
DMS Query on DMS Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B] mmCIF format, chain I [auth B]	I [auth B]	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain L [auth D] SDF format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain M [auth D]	L [auth D], M [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain L [auth D] Focus chain M [auth D]
NO3 Query on NO3 Download Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain K [auth C] MOL2 format, chain H [auth B] MOL2 format, chain K [auth C] mmCIF format, chain H [auth B] mmCIF format, chain K [auth C]	H [auth B], K [auth C]	NITRATE ION N O₃ NHNBFGGVMKEFGY-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain K [auth C] Interactions & Density Focus chain H [auth B] Focus chain K [auth C]