4WHU | pdb_00004whu

BROMO domain of CREB binding protein

PDB DOI: https://doi.org/10.2210/pdb4WHU/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2014-09-23 Released: 2015-10-28
Deposition Author(s): Liu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free:
0.261 (Depositor), 0.263 (DCC)
R-Value Work:
0.208 (Depositor), 0.220 (DCC)
R-Value Observed:
0.210 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Direct photocapture of bromodomains using tropolone chemical probes

Hett, E.C., Piatnitski Chekler, E.L., Basak, A., Bonin, P.D., Denny, R.A., Flick, A.C., Geoghegan, K.F., Liu, S., Pletcher, M.T., Robinson, R.P., Sahasrabudhe, P., Salter, S., Stock, I.A., Jones, L.H.

To be published.

Macromolecule Content

Total Structure Weight: 14.69 kDa
Atom Count: 1,038
Modeled Residue Count: 119
Deposited Residue Count: 119
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A	119	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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3OT Query on 3OT 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]	2-methoxy-4-{1-[2-(morpholin-4-yl)ethyl]-2-(2-phenylethyl)-1H-benzimidazol-5-yl}cyclohepta-2,4,6-trien-1-one C₂₉ H₃₁ N₃ O₃ ZSTNBLSPAMZIQD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
3OT	BindingDB: 4WHU	IC50: 210 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.261 (Depositor), 0.263 (DCC)
R-Value Work: 0.208 (Depositor), 0.220 (DCC)
R-Value Observed: 0.210 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 25.284	α = 90
b = 43.317	β = 98.68
c = 51.387	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement

Structure Validation

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Entry History

Deposition Data

Released Date: 2015-10-28

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-10-28
Type: Initial release
Version 1.1: 2023-09-27
Changes: Data collection, Database references, Derived calculations, 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.