3KC3 | pdb_00003kc3

MK2 complexed to inhibitor N4-(7-(benzofuran-2-yl)-1H-indazol-5-yl)pyrimidine-2,4-diamine

PDB DOI: https://doi.org/10.2210/pdb3KC3/pdb

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

Deposited: 2009-10-20 Released: 2010-01-12
Deposition Author(s): Argiriadi, M.A., Talanian, R.V., Borhani, D.W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free:
0.298 (Depositor), 0.288 (DCC)
R-Value Work:
0.230 (Depositor), 0.219 (DCC)
R-Value Observed:
0.233 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

2,4-Diaminopyrimidine MK2 inhibitors. Part I: Observation of an unexpected inhibitor binding mode.

Argiriadi, M.A., Ericsson, A.M., Harris, C.M., Banach, D.L., Borhani, D.W., Calderwood, D.J., Demers, M.D., Dimauro, J., Dixon, R.W., Hardman, J., Kwak, S., Li, B., Mankovich, J.A., Marcotte, D., Mullen, K.D., Ni, B., Pietras, M., Sadhukhan, R., Sousa, S., Tomlinson, M.J., Wang, L., Xiang, T., Talanian, R.V.

(2010) Bioorg Med Chem Lett 20: 330-333

PubMed: 19919896 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2009.10.102

PubMed Abstract:
MK2 is a Ser/Thr kinase of significant interest as an anti-inflammatory drug discovery target. Here we describe the development of in vitro tools for the identification and characterization of MK2 inhibitors, including validation of inhibitor interactions with the crystallography construct and determination of the unique binding mode of 2,4-diaminopyrimidine inhibitors in the MK2 active site. Use of these tools in the optimization of a potent and selective inhibitor lead series is described in the accompanying Letter.

Organizational Affiliation

Abbott Laboratories, 100 Research Drive, Worcester, MA 01605-5314, USA.

Macromolecule Content

Total Structure Weight: 454.02 kDa
Atom Count: 28,159
Modeled Residue Count: 3,428
Deposited Residue Count: 3,888
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP kinase-activated protein kinase 2	A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L	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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P49137
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MK2 Query on MK2 Download:Ideal Coordinates CCD File SDF format, chain W [auth L] SDF format, chain V [auth K] SDF format, chain U [auth J] SDF format, chain T [auth I] SDF format, chain S [auth H] SDF format, chain R [auth F] SDF format, chain Q [auth E] SDF format, chain P [auth D] SDF format, chain O [auth C] SDF format, chain N [auth B] SDF format, chain M [auth A] MOL2 format, chain W [auth L] MOL2 format, chain V [auth K] MOL2 format, chain U [auth J] MOL2 format, chain T [auth I] MOL2 format, chain S [auth H] MOL2 format, chain R [auth F] MOL2 format, chain Q [auth E] MOL2 format, chain P [auth D] MOL2 format, chain O [auth C] MOL2 format, chain N [auth B] MOL2 format, chain M [auth A] mmCIF format, chain W [auth L] mmCIF format, chain V [auth K] mmCIF format, chain U [auth J] mmCIF format, chain T [auth I] mmCIF format, chain S [auth H] mmCIF format, chain R [auth F] mmCIF format, chain Q [auth E] mmCIF format, chain P [auth D] mmCIF format, chain O [auth C] mmCIF format, chain N [auth B] mmCIF format, chain M [auth A]	M [auth A] N [auth B] O [auth C] P [auth D] Q [auth E] M [auth A], N [auth B], O [auth C], P [auth D], Q [auth E], R [auth F], S [auth H], T [auth I], U [auth J], V [auth K], W [auth L]	N~4~-[7-(1-benzofuran-2-yl)-1H-indazol-5-yl]pyrimidine-2,4-diamine C₁₉ H₁₄ N₆ O IQDDLNJTLVXFQA-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth H] Focus chain T [auth I] Focus chain U [auth J] Focus chain V [auth K] Focus chain W [auth L] Interactions & Density Focus chain M [auth A] Focus chain N [auth B] Focus chain O [auth C] Focus chain P [auth D] Focus chain Q [auth E] Focus chain R [auth F] Focus chain S [auth H] Focus chain T [auth I] Focus chain U [auth J] Focus chain V [auth K] Focus chain W [auth L]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.90 Å
R-Value Free: 0.298 (Depositor), 0.288 (DCC)
R-Value Work: 0.230 (Depositor), 0.219 (DCC)
R-Value Observed: 0.233 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 139.351	α = 90
b = 179.793	β = 90
c = 214.376	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	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: 2010-01-12

Deposition Author(s):

Argiriadi, M.A.

Talanian, R.V.

Borhani, D.W.

Revision History (Full details and data files)

Version 1.0: 2010-01-12
Type: Initial release
Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance
Version 1.2: 2024-02-21
Changes: Data collection, Database references, Derived calculations

3KC3 | pdb_00003kc3

MK2 complexed to inhibitor N4-(7-(benzofuran-2-yl)-1H-indazol-5-yl)pyrimidine-2,4-diamine

Literature

2,4-Diaminopyrimidine MK2 inhibitors. Part I: Observation of an unexpected inhibitor binding mode.

Biological Assembly 1

Biological Assembly 2

Biological Assembly 3

Biological Assembly 4

Biological Assembly 5

Macromolecules

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

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