3M42

Crystal structure of MAPKAP kinase 2 (MK2) complexed with a tetracyclic ATP site inhibitor

PDB DOI: https://doi.org/10.2210/pdb3M42/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): Yes

Deposited: 2010-03-10 Released: 2011-03-23
Deposition Author(s): Scheufler, C., Revesz, L., Be, C., Izaac, A., Huppertz, C., Schlapbach, A., Kroemer, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free:
0.232 (Depositor), 0.230 (DCC)
R-Value Work:
0.186 (Depositor), 0.180 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Novel pyrrolo[2,3-f]isoquinoline based MAPKAP-K2 (MK2) inhibitors with potent in vitro and in vivo activity

Revesz, L., Schlapbach, A., Aichholz, R., Feifel, R., Hawtin, S., Heng, R., Hiestand, P., Jahnke, W., Koch, G., Moebitz, H., Scheufler, C., Velcicky, J., Huppertz, C.

To be published.

Macromolecule Content

Total Structure Weight: 34.98 kDa
Atom Count: 2,479
Modelled Residue Count: 290
Deposited Residue Count: 299
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP kinase-activated protein kinase 2	A	299	Homo sapiens	Mutation(s): 1 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49137
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HGF Query on HGF Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	2-[5-(2-methoxyethoxy)pyridin-3-yl]-8,9,10,11-tetrahydro-7H-pyrido[3',4':4,5]pyrrolo[2,3-f]isoquinolin-7-one C₂₂ H₂₀ N₄ O₃ ZYTDQGRQFPNBGA-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
HGF	BindingDB: 3M42	IC50: min: 10, max: 1500 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.68 Å
R-Value Free: 0.232 (Depositor), 0.230 (DCC)
R-Value Work: 0.186 (Depositor), 0.180 (DCC)

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.2	α = 90
b = 103.2	β = 90
c = 166.6	γ = 120

Software Package:

Software Name	Purpose
CNX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2011-03-23

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-03-23
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-06
Changes: Database references, Derived calculations
Version 1.3: 2024-02-21
Changes: Data collection

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.