4M7I | pdb_00004m7i

Crystal Structure of GSK6157 Bound to PERK (R587-R1092, delete A660-T867) at 2.34A Resolution

PDB DOI: https://doi.org/10.2210/pdb4M7I/pdb

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

Deposited: 2013-08-12 Released: 2014-09-03
Deposition Author(s): Gampe, R.T., Axten, J.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free:
0.282 (Depositor), 0.275 (DCC)
R-Value Work:
0.207 (Depositor), 0.202 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Discovery of 5-{4-fluoro-1-[(6-methyl-2-pyridinyl)acetyl]-2,3-dihydro-1H-indol-5-yl}-7-methyl-7H-pyrrolo[2,3-d]pyrimidin-4-amine (GSK2656157), a Potent and Selective PERK Inhibitor Selected for Preclinical Development

Axten, J.M., Romeril, S.P., Shu, A., Ralph, J., Medina, J.R., Feng, Y., Li, W.H.H., Grant, S.W., Heerding, D.A., Minthorn, E., Mencken, T., Gaul, N., Goetz, A., Stanley, T., Hassell, A.M., Gampe, R.T., Atkins, C., Kumar, R.

To be published.

Macromolecule Content

Total Structure Weight: 35.21 kDa
Atom Count: 2,129
Modeled Residue Count: 247
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Eukaryotic translation initiation factor 2-alpha kinase 3	A	299	Homo sapiens	Mutation(s): 0 Gene Names: EIF2AK3, PEK, PERK EC: 2.7.11.1 (PDB Primary Data), 2.7.10.2 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NZJ5 (Homo sapiens) Explore Q9NZJ5 Go to UniProtKB: Q9NZJ5
PHAROS: Q9NZJ5 GTEx: ENSG00000172071
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9NZJ5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
27D Query on 27D 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]	1-[5-(4-amino-7-methyl-7H-pyrrolo[2,3-d]pyrimidin-5-yl)-4-fluoro-1H-indol-1-yl]-2-(6-methylpyridin-2-yl)ethanone C₂₃ H₁₉ F N₆ O YGEJQNSKXJFIJF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.34 Å
R-Value Free: 0.282 (Depositor), 0.275 (DCC)
R-Value Work: 0.207 (Depositor), 0.202 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.06	α = 90
b = 101.06	β = 90
c = 158.028	γ = 120

Software Package:

Software Name	Purpose
MD2	data collection
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2014-09-03

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2014-09-03
Type: Initial release
Version 1.1: 2017-08-23
Changes: Source and taxonomy
Version 1.2: 2017-11-15
Changes: Refinement description
Version 1.3: 2023-09-20
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.