3PG3

Human p38 MAP Kinase in Complex with RL182

PDB DOI: https://doi.org/10.2210/pdb3PG3/pdb

Classification: TRANSFERASE/TRANSFERASE INHIBITOR
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2010-10-29 Released: 2011-11-02
Deposition Author(s): Gruetter, C., Simard, J.R., Getlik, M., Rauh, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.261
R-Value Work: 0.220
R-Value Observed: 0.221

wwPDB Validation 3D Report Full Report

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

Literature

Structure-based design and synthesis of cell active N-pyrazole, N-thiazole urea inhibitors of the MAP kinase p38alpha

Getlik, M., Gruetter, C., Simard, J.R., Van Otterlo, W., Robubi, A., Aust, B., Rauh, D.

To be published.

Macromolecule Content

Total Structure Weight: 42.02 kDa
Atom Count: 2,875
Modelled Residue Count: 337
Deposited Residue Count: 360
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	360	Homo sapiens	Mutation(s): 4 Gene Names: MAPK14, CSBP, CSBP1, CSBP2, CSPB1, MXI2, SAPK2A 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q16539
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DG7 Query on DG7 Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	1-[3-tert-butyl-1-(4-methylphenyl)-1H-pyrazol-5-yl]-3-{4-[2-(pyridin-3-ylmethoxy)ethyl]-1,3-thiazol-2-yl}urea C₂₆ H₃₀ N₆ O₂ S FNKUETGWXHXSHJ-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
BOG Query on BOG Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A]	B [auth A]	octyl beta-D-glucopyranoside C₁₄ H₂₈ O₆ HEGSGKPQLMEBJL-RKQHYHRCSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
DG7	BindingDB: 3PG3	Kd: 1656 (nM) from 1 assay(s)
DG7	BindingDB: 3PG3	IC50: 3641 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.261
R-Value Work: 0.220
R-Value Observed: 0.221
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.11	α = 90
b = 69.97	β = 90
c = 74.53	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

View Full Validation Report

Entry History

Deposition Data

Released Date: 2011-11-02

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2011-11-02
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: 2023-09-06
Changes: Data collection, Database references, Refinement description, Structure summary

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Help and Resources

3PG3

Human p38 MAP Kinase in Complex with RL182

Structure-based design and synthesis of cell active N-pyrazole, N-thiazole urea inhibitors of the MAP kinase p38alpha

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Deposition Data

Revision History (Full details and data files)