3FLN

P38 kinase crystal structure in complex with R1487

PDB DOI: https://doi.org/10.2210/pdb3FLN/pdb

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

Deposited: 2008-12-19 Released: 2009-12-22
Deposition Author(s): Kuglstatter, A., Knapp, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.234
R-Value Work: 0.210
R-Value Observed: 0.211

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

The Discovery of Pamapimod, R1503 and R1487 as Orally Bioavailable and Highly Selective Inhibitors of p38 Map Kinase

Soth, M., Kuglstatter, A., Goldstein, D.

To be published.

Macromolecule Content

Total Structure Weight: 43.11 kDa
Atom Count: 3,153
Modelled Residue Count: 343
Deposited Residue Count: 372
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A [auth C]	372	Homo sapiens	Mutation(s): 1 Gene Names: CSBP, CSBP1, CSBP2, CSPB1, MAPK14, 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16539
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
3FN Query on 3FN Download Ideal Coordinates CCD File SDF format, chain B [auth C] MOL2 format, chain B [auth C] mmCIF format, chain B [auth C]	B [auth C]	6-(2,4-difluorophenoxy)-8-methyl-2-(tetrahydro-2H-pyran-4-ylamino)pyrido[2,3-d]pyrimidin-7(8H)-one C₁₉ H₁₈ F₂ N₄ O₃ KKKRKRMVJRHDMG-UHFFFAOYSA-N		Interactions Focus chain B [auth C] Interactions & Density Focus chain B [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
3FN	BindingDB: 3FLN	Kd: 0.2 (nM) from 1 assay(s)
3FN	BindingDB: 3FLN	IC50: 10 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.90 Å
R-Value Free: 0.234
R-Value Work: 0.210
R-Value Observed: 0.211
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.699	α = 90
b = 85.88	β = 90
c = 124.793	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CNS	refinement
ADSC	data collection
MOSFLM	data reduction
SCALA	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-12-22

Deposition Author(s):

Kuglstatter, A.

Revision History (Full details and data files)

Version 1.0: 2009-12-22
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2019-07-24
Changes: Data collection, Refinement description
Version 1.3: 2021-10-20
Changes: Database references, Derived calculations
Version 1.4: 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.