6ALC | pdb_00006alc

CREBBP bromodomain in complex with Cpd 4 (1-(1-(cyclopropylmethyl)-3-(1H-indol-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl)ethan-1-one)

• PDB DOI: https://doi.org/10.2210/pdb6ALC/pdb

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


• Deposited: 2017-08-07 Released: 2018-08-08 
• Deposition Author(s): Murray, J.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free: 
  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 
  0.190 (Depositor) 

Starting Model: experimental

Literature

Design and synthesis of a biaryl series as inhibitors for the bromodomains of CBP/P300.

Lai, K.W., Romero, F.A., Tsui, V., Beresini, M.H., de Leon Boenig, G., Bronner, S.M., Chen, K., Chen, Z., Choo, E.F., Crawford, T.D., Cyr, P., Kaufman, S., Li, Y., Liao, J., Liu, W., Ly, J., Murray, J., Shen, W., Wai, J., Wang, F., Zhu, C., Zhu, X., Magnuson, S.

(2018) Bioorg Med Chem Lett 28: 15-23

• PubMed: 29169673 
• DOI: https://doi.org/10.1016/j.bmcl.2017.11.025
• Primary Citation Related Structures: 
  6ALC


• PubMed Abstract: 
  

  A novel, potent, and orally bioavailable inhibitor of the bromodomain of CBP, compound 35 (GNE-207), has been identified through SAR investigations focused on optimizing al bicyclic heteroarene to replace the aniline present in the published GNE-272 series. Compound 35 has excellent CBP potency (CBP IC ₅₀  = 1 nM, MYC EC ₅₀  = 18 nM), a selectively index of >2500-fold against BRD4(1), and exhibits a good pharmacokinetic profile.

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Organizational Affiliation: 
• WuXi AppTec Co., Ltd., 288 Fute Zhong Road, Waigaoqiao Free Trade Zone, Shanghai 200131, People's Republic of China.
Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States.
Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States. Electronic address: [e-mail].
Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 27.57 kDa 
• Atom Count: 2,215 
• Modeled Residue Count: 228 
• Deposited Residue Count: 228 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CREB-binding protein	A, B	114	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BKD	E [auth B]	1-[1-(cyclopropylmethyl)-3-(1H-indol-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]ethan-1-one C20 H22 N4 O MPXKOIKIRQBXKT-UHFFFAOYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
EDO	D [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
BKD	BindingDB:  6ALC	IC50: 31 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.39 Å
• R-Value Free:  0.212 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.189 (Depositor), 0.189 (DCC) 
• R-Value Observed: 0.190 (Depositor) 

Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 124.924	α = 90
b = 124.924	β = 90
c = 40.241	γ = 120

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Murray, J.M.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Database references
• Version 1.2: 2023-10-04
  Changes: Data collection, Database references, Refinement description