5N2L | pdb_00005n2l

Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline analogue

PDB DOI: https://doi.org/10.2210/pdb5N2L/pdb

Deposited: 2017-02-07 Released: 2018-02-28
Deposition Author(s): Tallant, C., Slavish, P.J., Siejka, P., Bharatham, N., Shadrick, W.R., Chai, S., Young, B.M., Boyd, V.A., Heroven, C., Wiggers, H.J., Picaud, S., Fedorov, O., Krojer, T., Chen, T., Lee, R.E., Guy, R.K., Shelat, A.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free:
0.233 (Depositor), 0.235 (DCC)
R-Value Work:
0.181 (Depositor), 0.190 (DCC)
R-Value Observed:
0.184 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of the second bromodomain of human BRD2 in complex with a tetrahydroquinoline analogue

Tallant, C., Slavish, P.J., Siejka, P., Bharatham, N., Shadrick, W.R., Chai, S., Young, B.M., Boyd, V.A., Heroven, C., Wiggers, H.J., Picaud, S., Fedorov, O., Krojer, T., Chen, T., Lee, R.E., Guy, R.K., Shelat, A.A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S.

To be published.

Macromolecule Content

Total Structure Weight: 56.02 kDa
Atom Count: 4,074
Modeled Residue Count: 433
Deposited Residue Count: 456
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 2	A, B, C, D	114	Homo sapiens	Mutation(s): 0 Gene Names: BRD2, KIAA9001, RING3
UniProt & NIH Common Fund Data Resources
Find proteins for P25440 (Homo sapiens) Explore P25440 Go to UniProtKB: P25440
PHAROS: P25440 GTEx: ENSG00000204256
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P25440
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
8J2 Query on 8J2 Download:Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain O [auth C] SDF format, chain P [auth C] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain O [auth C] MOL2 format, chain P [auth C] MOL2 format, chain L [auth B] mmCIF format, chain H [auth A] mmCIF format, chain O [auth C] mmCIF format, chain P [auth C] mmCIF format, chain L [auth B]	H [auth A], L [auth B], O [auth C], P [auth C]	propan-2-yl ~{N}-[(2~{S},4~{R})-6-(3-acetamidophenyl)-1-ethanoyl-2-methyl-3,4-dihydro-2~{H}-quinolin-4-yl]carbamate C₂₄ H₂₉ N₃ O₄ UIHJJMSWZNYBQU-OYHNWAKOSA-N		Interactions Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C] Interactions & Density Focus chain H [auth A] Focus chain L [auth B] Focus chain O [auth C] Focus chain P [auth C]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain I [auth B] SDF format, chain K [auth B] SDF format, chain M [auth C] SDF format, chain Q [auth D] SDF format, chain J [auth B] MOL2 format, chain E [auth A] MOL2 format, chain I [auth B] MOL2 format, chain K [auth B] MOL2 format, chain M [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain J [auth B] mmCIF format, chain E [auth A] mmCIF format, chain I [auth B] mmCIF format, chain K [auth B] mmCIF format, chain M [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain J [auth B]	E [auth A] I [auth B] J [auth B] K [auth B] M [auth C] E [auth A], I [auth B], J [auth B], K [auth B], M [auth C], Q [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain Q [auth D] Interactions & Density Focus chain E [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain K [auth B] Focus chain M [auth C] Focus chain Q [auth D]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain R [auth D] SDF format, chain N [auth C] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain R [auth D] MOL2 format, chain N [auth C] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain R [auth D] mmCIF format, chain N [auth C]	F [auth A], G [auth A], N [auth C], R [auth D]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth C] Focus chain R [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain N [auth C] Focus chain R [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.89 Å
R-Value Free: 0.233 (Depositor), 0.235 (DCC)
R-Value Work: 0.181 (Depositor), 0.190 (DCC)
R-Value Observed: 0.184 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 147.244	α = 90
b = 94.409	β = 95.43
c = 38.585	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2018-02-28

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2018-02-28
Type: Initial release
Version 1.1: 2018-10-03
Changes: Data collection
Version 1.2: 2024-01-17
Changes: Data collection, Database references, Refinement description