3GP0

Crystal Structure of Human Mitogen Activated Protein Kinase 11 (p38 beta) in complex with Nilotinib

• PDB DOI: https://doi.org/10.2210/pdb3GP0/pdb

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


• Deposited: 2009-03-20 Released: 2009-04-07 
• Deposition Author(s): Filippakopoulos, P., Barr, A., Fedorov, O., Keates, T., Soundararajan, M., Elkins, J., Salah, E., Burgess-Brown, N., Ugochukwu, E., Pike, A.C.W., Muniz, J., Roos, A., Chaikuad, A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.232 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 

Starting Models: experimental

Literature

Crystal Structure of Human Mitogen Activated Protein Kinase 11 (p38 beta) in complex with Nilotinib

Filippakopoulos, P., Barr, A., Fedorov, O., Keates, T., Soundararajan, M., Elkins, J., Salah, E., Burgess-Brown, N., Ugochukwu, E., Pike, A.C.W., Muniz, J., Roos, A., Chaikuad, A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

To be published.

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: 40.38 kDa 
• Atom Count: 2,929 
• Modelled Residue Count: 333 
• Deposited Residue Count: 348 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 11	A	348	Homo sapiens	Mutation(s): 0  Gene Names: MAPK11, PRKM11, SAPK2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q15759 (Homo sapiens) Explore Q15759  Go to UniProtKB:  Q15759
PHAROS:  Q15759 GTEx:  ENSG00000185386

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NIL	B [auth A]	Nilotinib C28 H22 F3 N7 O HHZIURLSWUIHRB-UHFFFAOYSA-N
EDO	C [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	D [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
NIL	PDBBind:  3GP0	Kd: 36 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.90 Å
• R-Value Free: 0.232 
• R-Value Work: 0.178 
• R-Value Observed: 0.181 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 38.94	α = 90
b = 60.08	β = 90
c = 148.55	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-07 
Deposition Author(s): Filippakopoulos, P., Barr, A., Fedorov, O., Keates, T., Soundararajan, M., Elkins, J., Salah, E., Burgess-Brown, N., Ugochukwu, E., Pike, A.C.W., Muniz, J., Roos, A., Chaikuad, A., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Weigelt, J., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Revision History  

• Version 1.0: 2009-04-07
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description