7SSK | pdb_00007ssk

Human P300 complexed with a glycine-based inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.235 (Depositor), 0.235 (DCC) 
  • R-Value Work: 
    0.187 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 7SSK

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Discovery of Proline-Based p300/CBP Inhibitors Using DNA-Encoded Library Technology in Combination with High-Throughput Screening.

Tian, X.Suarez, D.Thomson, D.Li, W.King, E.A.LaFrance, L.Boehm, J.Barton, L.Di Marco, C.Martyr, C.Thalji, R.Medina, J.Knight, S.Heerding, D.Gao, E.Nartey, E.Cecconie, T.Nixon, C.Zhang, G.Berrodin, T.J.Phelps, C.Patel, A.Bai, X.Lind, K.Prabhu, N.Messer, J.Zhu, Z.Shewchuk, L.Reid, R.Graves, A.P.McHugh, C.Mangatt, B.

(2022) J Med Chem 65: 14391-14408

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00670
  • Primary Citation Related Structures: 
    7SS8, 7SSK, 7SZQ

  • PubMed Abstract: 

    E1A binding protein (p300) and CREB binding protein (CBP) are two highly homologous and multidomain histone acetyltransferases. These two proteins are involved in many cellular processes by acting as coactivators of a large number of transcription factors. Dysregulation of p300/CBP has been found in a variety of cancers and other diseases, and inhibition has been shown to decrease Myc expression. Herein, we report the identification of a series of highly potent, proline-based small-molecule p300/CBP histone acetyltransferase (HAT) inhibitors using DNA-encoded library technology in combination with high-throughput screening. The strategy of reducing ChromlogD and fluorination of metabolic soft spots was explored to improve the pharmacokinetic properties of potent p300 inhibitors. Fluorination of both cyclobutyl and proline rings of 22 led to not only reduced clearance but also improved cMyc cellular potency.


  • Organizational Affiliation
    • Research and Development, GlaxoSmithKline, 1250 South Collegeville Road, Collegeville, Pennsylvania 19426, United States.

Macromolecule Content 

  • Total Structure Weight: 66.81 kDa 
  • Atom Count: 4,130 
  • Modeled Residue Count: 482 
  • Deposited Residue Count: 569 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Histone acetyltransferase p300569Homo sapiensMutation(s): 1 
EC: 2.3.1.48 (PDB Primary Data), 2.3.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q09472 (Homo sapiens)
Explore Q09472 
Go to UniProtKB:  Q09472
PHAROS:  Q09472
GTEx:  ENSG00000100393 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ09472
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
C3I
(Subject of Investigation/LOI)

Query on C3I



Download:Ideal Coordinates CCD File
E [auth A]N-[2-(4-methoxyanilino)-2-oxoethyl]-N-methyl-1-phenylcyclopentane-1-carboxamide
C22 H26 N2 O3
DKCHMKRLQSFONS-UHFFFAOYSA-N
ZN

Query on ZN



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO

Query on EDO



Download:Ideal Coordinates CCD File
D [auth A]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
ACT

Query on ACT



Download:Ideal Coordinates CCD File
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.235 (Depositor), 0.235 (DCC) 
  • R-Value Work:  0.187 (Depositor), 0.192 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 63.878α = 90
b = 48.772β = 101.18
c = 109.353γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not fundedUnited States--

Revision History  (Full details and data files)

  • Version 1.0: 2022-11-09
    Type: Initial release
  • Version 1.1: 2022-11-16
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description