4TYH | pdb_00004tyh

Ternary complex of P38 and MK2 with a P38 inhibitor

PDB DOI: https://doi.org/10.2210/pdb4TYH/pdb

Classification: Transferase/Transferase inhibitor
Organism(s): Homo sapiens, Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2014-07-08 Released: 2015-07-22
Deposition Author(s): Cumming, J.G., Debreczeni, J.E., Edfeldt, F., Evertsson, F., Harrison, M., Holdgate, G., James, M., Lamont, S., Oldham, K., Sullivan, J.E., Wells, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free:
0.313 (Depositor), 0.300 (DCC)
R-Value Work:
0.228 (Depositor), 0.230 (DCC)
R-Value Observed:
0.232 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Discovery of substrate selective, ATP-competitive P38 alpha MAP kinase inhibitors

Cumming, J.G.

To be published.

Macromolecule Content

Total Structure Weight: 80.67 kDa
Atom Count: 5,442
Modeled Residue Count: 674
Deposited Residue Count: 698
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MAP kinase-activated protein kinase 2	A	350	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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P49137
Sequence Annotations Expand
Reference Sequence LOADING

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	B	348	Mus musculus	Mutation(s): 0 Gene Names: Mapk14, Crk1, Csbp1, Csbp2 EC: 2.7.11.24
UniProt
Find proteins for P47811 (Mus musculus) Explore P47811 Go to UniProtKB: P47811
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P47811
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
39G Query on 39G Download Ideal Coordinates CCD File SDF format, chain C [auth B] MOL2 format, chain C [auth B] mmCIF format, chain C [auth B]	C [auth B]	N-[5-(dimethylsulfamoyl)-2-methylphenyl]-1-phenyl-5-propyl-1H-pyrazole-4-carboxamide C₂₂ H₂₆ N₄ O₃ S MOBKKWWSLMVASV-UHFFFAOYSA-N		Interactions Focus chain C [auth B] Interactions & Density Focus chain C [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
39G	BindingDB: 4TYH	Ki: 14 (nM) from 1 assay(s)
		Kd: min: 1.54e+4, max: 1.55e+4 (nM) from 2 assay(s)
		IC50: min: 61, max: 1.00e+4 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.00 Å
R-Value Free: 0.313 (Depositor), 0.300 (DCC)
R-Value Work: 0.228 (Depositor), 0.230 (DCC)
R-Value Observed: 0.232 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.726	α = 90
b = 87.726	β = 90
c = 229.876	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-07-22

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2015-07-22
Type: Initial release
Version 1.1: 2023-12-27
Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Source and taxonomy