3A2C | pdb_00003a2c

Crystal structure of a pyrazolopyrimidine inhibitor complex bound to MAPKAP Kinase-2 (MK2)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 
    0.335 (Depositor), 0.267 (DCC) 
  • R-Value Work: 
    0.288 (Depositor), 0.213 (DCC) 

Starting Model: experimental
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This is version 1.2 of the entry. See complete history

Literature

Structural analysis of an MK2-inhibitor complex: insight into the regulation of the secondary structure of the Gly-rich loop by TEI-I01800

Fujino, A.Fukushima, K.Namiki, N.Kosugi, T.Takimoto-Kamimura, M.

(2010) Acta Crystallogr D Biol Crystallogr 66: 80-87

  • DOI: https://doi.org/10.1107/S0907444909046411
  • Primary Citation Related Structures: 
    3A2C

  • PubMed Abstract: 

    Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAP-K2 or MK2) is a Ser/Thr kinase from the p38 mitogen-activated protein kinase signalling pathway and plays an important role in inflammatory diseases. The crystal structure of the complex of human MK2 (residues 41-364) with the potent MK2 inhibitor TEI-I01800 (pK(i) = 6.9) was determined at 2.9 A resolution. The MK2 structure in the MK2-TEI-I01800 complex is composed of two domains, as observed for other Ser/Thr kinases; however, the Gly-rich loop in the N-terminal domain forms an alpha-helix structure and not a beta-sheet. TEI-I01800 binds to the ATP-binding site as well as near the substrate-binding site of MK2. Both TEI-I01800 molecules have a nonplanar conformation that differs from those of other MK2 inhibitors deposited in the Protein Data Bank. The MK2-TEI-I01800 complex structure is the first active MK2 with an alpha-helical Gly-rich loop and TEI-I01800 regulates the secondary structure of the Gly-rich loop.


  • Organizational Affiliation
    • Teijin Institute for Biomedical Research, Japan.

Macromolecule Content 

  • Total Structure Weight: 459.15 kDa 
  • Atom Count: 27,440 
  • Modeled Residue Count: 3,311 
  • Deposited Residue Count: 3,888 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
MAP kinase-activated protein kinase 2
A, B, C, D, E
A, B, C, D, E, F, G, H, I, J, K, L
324Homo sapiensMutation(s): 0 
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49137
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PDY

Query on PDY



Download:Ideal Coordinates CCD File
AA [auth G]
BA [auth H]
CA [auth H]
DA [auth I]
EA [auth I]
AA [auth G],
BA [auth H],
CA [auth H],
DA [auth I],
EA [auth I],
FA [auth J],
GA [auth J],
HA [auth K],
IA [auth K],
JA [auth L],
KA [auth L],
M [auth A],
N [auth A],
O [auth B],
P [auth B],
Q [auth C],
R [auth C],
S [auth D],
T [auth D],
U [auth E],
V [auth E],
W [auth F],
X [auth F],
Z [auth G]
N~7~-(4-ethoxyphenyl)-6-methyl-N~5~-[(3S)-piperidin-3-yl]pyrazolo[1,5-a]pyrimidine-5,7-diamine
C20 H26 N6 O
WJOUGMPFYANZMI-INIZCTEOSA-N
SO4

Query on SO4



Download:Ideal Coordinates CCD File
Y [auth F]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free:  0.335 (Depositor), 0.267 (DCC) 
  • R-Value Work:  0.288 (Depositor), 0.213 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 139.157α = 90
b = 180.956β = 90
c = 216.096γ = 90
Software Package:
Software NamePurpose
CNXrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-12
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description