2PZY | pdb_00002pzy

Structure of MK2 Complexed with Compound 76

• PDB DOI: https://doi.org/10.2210/pdb2PZY/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2007-05-18 Released: 2007-07-31 
• Deposition Author(s): White, A., Wu, J.P., Wang, J., Abeywardane, A., Andersen, D., Emmanuel, M., Gautschi, E., Goldberg, D.R., Kashem, M.A., Lukas, S., Mao, W., Martin, L., Morwick, T., Moss, N., Pargellis, C., Patel, U.R., Patnaude, L., Peet, G.W., Skow, D., Snow, R.J., Ward, Y., Werneburg, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 
  0.313 (Depositor) 
• R-Value Work: 
  0.251 (Depositor) 

Literature

The discovery of carboline analogs as potent MAPKAP-K2 inhibitors

Wu, J.-P., Wang, J., Abeywardane, A., Andersen, D., Emmanuel, M., Gautschi, E., Goldberg, D.R., Kashem, M.A., Lukas, S., Mao, W., Martin, L., Morwick, T., Moss, N., Pargellis, C., Patel, U.R., Patnaude, L., Peet, G.W., Skow, D., Snow, R.J., Ward, Y., Werneburg, B., White, A.

(2007) Bioorg Med Chem Lett 17: 4664-4669

• PubMed: 17576063 
• DOI: https://doi.org/10.1016/j.bmcl.2007.05.101
• Primary Citation Related Structures: 
  2PZY


• PubMed Abstract: 
  

  The discovery of a series of potent, carboline-based MK2 inhibitors is described. These compounds inhibit MK2 with IC50s as low as 10 nM, as measured in a DELFIA assay. An X-ray crystal structure reveals that they bind in a region near the p-loop and the hinge region of MK2a.

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Organizational Affiliation: 
• Research and Development, Boehringer-Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT 06877, USA. [e-mail]

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

Biological assembly 4 assigned by authors.

Biological Assembly 5  

Global Symmetry: Tetrahedral - T  (Explore in 3D)
Global Stoichiometry: Homo 12-mer - A12 

Biological assembly 5 generated by PISA,PQS (software)

Macromolecule Content 

• Total Structure Weight: 151.43 kDa 
• Atom Count: 9,585 
• Modeled Residue Count: 1,169 
• Deposited Residue Count: 1,296 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP kinase-activated protein kinase 2	A, B, C, D	324	Homo sapiens	Mutation(s): 0  Gene Names: MAPKAPK2 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P49137 (Homo sapiens) Explore P49137  Go to UniProtKB:  P49137
PHAROS:  P49137 GTEx:  ENSG00000162889

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
STU	G [auth C]	STAUROSPORINE C28 H26 N4 O3 HKSZLNNOFSGOKW-FYTWVXJKSA-N
B18	E [auth A], F [auth B]	(4R)-N-[4-({[2-(DIMETHYLAMINO)ETHYL]AMINO}CARBONYL)-1,3-THIAZOL-2-YL]-4-METHYL-1-OXO-2,3,4,9-TETRAHYDRO-1H-BETA-CARBOLINE-6-CARBOXAMIDE C21 H24 N6 O3 S QWFFPYQWUWLDBV-NSHDSACASA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
STU	BindingDB:  2PZY	IC50: 1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free:  0.313 (Depositor) 
• R-Value Work:  0.251 (Depositor) 

Space Group: P 6₃

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 159.61	α = 90
b = 159.61	β = 90
c = 134.5	γ = 120

Software Package:

Software Name	Purpose
d*TREK	data processing
CNS	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-07-31 
Deposition Author(s): White, A., Wu, J.P., Wang, J., Abeywardane, A., Andersen, D., Emmanuel, M., Gautschi, E., Goldberg, D.R., Kashem, M.A., Lukas, S., Mao, W., Martin, L., Morwick, T., Moss, N., Pargellis, C., Patel, U.R., Patnaude, L., Peet, G.W., Skow, D., Snow, R.J., Ward, Y., Werneburg, B.

Revision History  

• Version 1.0: 2007-07-31
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references