5BVD | pdb_00005bvd

Tetrahydropyrrolo-diazepenones as inhibitors of ERK2 kinase

• PDB DOI: https://doi.org/10.2210/pdb5BVD/pdb

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


• Deposited: 2015-06-05 Released: 2015-09-09 
• Deposition Author(s): Ma, X., Steven, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Tetrahydropyrrolo-diazepenones as inhibitors of ERK2 kinase.

Bagdanoff, J.T., Jain, R., Han, W., Zhu, S., Madiera, A.M., Lee, P.S., Ma, X., Poon, D.

(2015) Bioorg Med Chem Lett 25: 3788-3792

• PubMed: 26259804 
• DOI: https://doi.org/10.1016/j.bmcl.2015.07.091
• Primary Citation of Related Structures:  
  5BVD, 5BVE, 5BVF


• PubMed Abstract: 
  

  A series of structure based drug design hypotheses and focused screening efforts led to the identification of tetrahydropyrrolo-diazepenones with striking potency against ERK2 kinase. The role of fluorination in mitigating microsomal clearance was systematically explored. Ultimately, it was found that fluorination of a cyclopentanol substructure provided significant improvement in both potency and human metabolic stability.

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Organizational Affiliation: 

Global Discovery Chemistry/Oncology and Exploratory Chemistry, Novartis Institutes for BioMedical Research, 250 Massachusetts Ave., Cambridge, MA 02139, USA. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 42.42 kDa 
• Atom Count: 3,049 
• Modelled Residue Count: 330 
• Deposited Residue Count: 361 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 1	A	361	Homo sapiens	Mutation(s): 0  Gene Names: MAPK1, ERK2, PRKM1, PRKM2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for P28482 (Homo sapiens) Explore P28482  Go to UniProtKB:  P28482
PHAROS:  P28482 GTEx:  ENSG00000100030

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4VF	B [auth A]	2-[(1S)-1-(3-chlorophenyl)-2-hydroxyethyl]-7-[2-(tetrahydro-2H-pyran-4-ylamino)pyrimidin-4-yl]-3,4-dihydropyrrolo[1,2-a]pyrazin-1(2H)-one C24 H26 Cl N5 O3 PJPXAFCTLKCTJP-JOCHJYFZSA-N
SO4	C [auth A], D [auth A], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Binding Affinity Annotations
ID	Source	Binding Affinity
4VF	BindingDB:  5BVD	IC50: 0.16 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.170 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.271	α = 90
b = 71.282	β = 90
c = 120.451	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PROCESS	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-09 
Deposition Author(s): Ma, X., Steven, S.

Revision History  

• Version 1.0: 2015-09-09
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description