4NYW

Crystal Structure of the Bromodomain of human CREBBP in complex with a dihydroquinoxalinone ligand

PDB DOI: https://doi.org/10.2210/pdb4NYW/pdb

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

Deposited: 2013-12-11 Released: 2014-01-29
Deposition Author(s): Filippakopoulos, P., Picaud, S., Felletar, I., Rooney, T.P.C., Fedorov, O., Martin, S., Monteiro, O.P., Conway, S.J., von Delft, F., Brennan, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.187
R-Value Work: 0.163
R-Value Observed: 0.164

Starting Models: experimental
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This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of the Bromodomain of human CREBBP in complex with a dihydroquinoxalinone ligand

Filippakopoulos, P., Picaud, S., Felletar, I., Rooney, T.P.C., Fedorov, O., Martin, S., Monteiro, O.P., Conway, S.J., von Delft, F., Brennan, P., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 14.78 kDa
Atom Count: 1,214
Modelled Residue Count: 116
Deposited Residue Count: 119
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	119	Homo sapiens	Mutation(s): 0 Gene Names: CBP, CREBBP EC: 2.3.1 (UniProt), 2.3.1.48 (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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
2O3 Query on 2O3 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	(3R)-N-[3-(3,4-dihydroquinolin-1(2H)-yl)propyl]-3-methyl-2-oxo-1,2,3,4-tetrahydroquinoxaline-5-carboxamide C₂₂ H₂₆ N₄ O₂ XBNNWBHEMSYHTJ-OAHLLOKOSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
SCN Query on SCN Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	THIOCYANATE ION C N S ZMZDMBWJUHKJPS-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.43 Å
R-Value Free: 0.187
R-Value Work: 0.163
R-Value Observed: 0.164
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 34.966	α = 90
b = 49.917	β = 90
c = 80.16	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-01-29

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2014-01-29
Type: Initial release
Version 1.1: 2018-01-31
Changes: Database references, Structure summary
Version 1.2: 2023-09-20
Changes: Data collection, Database references, Derived calculations, Refinement description

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4NYW

Crystal Structure of the Bromodomain of human CREBBP in complex with a dihydroquinoxalinone ligand

Crystal Structure of the Bromodomain of human CREBBP in complex with a dihydroquinoxalinone ligand

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)