5LAR | pdb_00005lar

Crystal structure of p38 alpha MAPK14 in complex with VPC00628

PDB DOI: https://doi.org/10.2210/pdb5LAR/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2016-06-14 Released: 2016-07-06
Deposition Author(s): Chaikuad, A., Petersen, L.K., von Delft, F., Arrowsmith, C.H., Edwards, A.M., Bountra, C., Knapp, S., Structural Genomics Consortium (SGC)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free:
0.205 (Depositor), 0.205 (DCC)
R-Value Work:
0.169 (Depositor), 0.170 (DCC)
R-Value Observed:
0.171 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Novel p38alpha MAP kinase inhibitors identified from yoctoReactor DNA-encoded small molecule library

Petersen, L.K., Blakskaer, P., Chaikuad, A., Christensen, A.B., Dietvorst, J., Holmkvist, J., Knapp, S., Korinek, M., Larsen, L.K., Pedersen, A.E., Rohm, S., Slok, F.A., Hansen, N.J.V.

(2016) Medchemcomm 7: 1332-1339

DOI: https://doi.org/10.1039/C6MD00241B

Macromolecule Content

Total Structure Weight: 41.9 kDa
Atom Count: 3,297
Modeled Residue Count: 350
Deposited Residue Count: 361
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Mitogen-activated protein kinase 14	A	361	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P47811
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6SH Query on 6SH Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	5-azanyl-~{N}-[[4-[[(2~{S})-1-azanyl-4-cyclohexyl-1-oxidanylidene-butan-2-yl]carbamoyl]phenyl]methyl]-1-phenyl-pyrazole-4-carboxamide C₂₈ H₃₄ N₆ O₃ RXVCNLNARLCLHQ-DEOSSOPVSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.205 (Depositor), 0.205 (DCC)
R-Value Work: 0.169 (Depositor), 0.170 (DCC)
R-Value Observed: 0.171 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.019	α = 90
b = 70.58	β = 90
c = 75.029	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-07-06

Deposition Author(s):

Structural Genomics Consortium (SGC)

Revision History (Full details and data files)

Version 1.0: 2016-07-06
Type: Initial release
Version 1.1: 2016-08-03
Changes: Database references
Version 1.2: 2024-01-10
Changes: Data collection, Database references, Refinement description