3QUD | pdb_00003qud

Human p38 MAP Kinase in Complex with 2-amino-phenylamino-benzophenone

• PDB DOI: https://doi.org/10.2210/pdb3QUD/pdb

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


• Deposited: 2011-02-23 Released: 2012-04-11 
• Deposition Author(s): Gruetter, C., Rauh, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.278 (Depositor) 
• R-Value Work: 
  0.232 (Depositor) 
• R-Value Observed: 
  0.234 (Depositor) 

Starting Model: experimental

Literature

Resolving the selectivity problem for p38 mitogen activated protein (MAP) Kinase-inhibitors: Development of new highly potent inhibitors of p38 MAP kinase with an outstanding selectivity profile

Karcher, S.C., Fischer, S., Schattel, V., Romir, J., Stehle, T., Gruetter, C., Rauh, D., Laufer, S.A.

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: 42.14 kDa 
• Atom Count: 2,951 
• Modeled Residue Count: 345 
• Deposited Residue Count: 360 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	360	Homo sapiens	Mutation(s): 0  Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2 EC: 2.7.11.24
UniProt & NIH Common Fund Data Resources
Find proteins for Q16539 (Homo sapiens) Explore Q16539  Go to UniProtKB:  Q16539
PHAROS:  Q16539 GTEx:  ENSG00000112062

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BOG	B [auth A], D [auth A]	octyl beta-D-glucopyranoside C14 H28 O6 HEGSGKPQLMEBJL-RKQHYHRCSA-N
N3F	C [auth A]	{4-[(2-aminophenyl)amino]phenyl}(phenyl)methanone C19 H16 N2 O RAWYMBACZSQNDD-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
N3F	BindingDB:  3QUD	IC50: 145 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.278 (Depositor) 
• R-Value Work:  0.232 (Depositor) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.779	α = 90
b = 73.368	β = 90
c = 79.591	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-04-11 
Deposition Author(s): Gruetter, C., Rauh, D.

Revision History  

• Version 1.0: 2012-04-11
  Type: Initial release
  
• Version 1.1: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Refinement description, Structure summary