5MZ3

P38 ALPHA MUTANT C162S IN COMPLEX WITH CMPD2 [N-(4-Methyl-3-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)phenyl)-3-(trifluoromethyl)benzamide]

PDB DOI: https://doi.org/10.2210/pdb5MZ3/pdb

Classification: TRANSFERASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2017-01-30 Released: 2017-11-15
Deposition Author(s): Cowan-Jacob, S.W., Scheufler, C.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.197
R-Value Work: 0.165
R-Value Observed: 0.166

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Imidazo[1,2-a]pyridin-6-yl-benzamide analogs as potent RAF inhibitors.

Smith, A., Ni, Z.J., Poon, D., Huang, Z., Chen, Z., Zhang, Q., Tandeske, L., Merritt, H., Shoemaker, K., Chan, J., Kaufman, S., Huh, K., Murray, J., Appleton, B.A., Cowan-Jacob, S.W., Scheufler, C., Kanazawa, T., Jansen, J.M., Stuart, D., Shafer, C.M.

(2017) Bioorg Med Chem Lett 27: 5221-5224

PubMed: 29107542 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2017.10.047
Primary Citation of Related Structures:
5MZ3, 6B8U

PubMed Abstract:
A series of imidazo[1,2-a]pyridin-6-yl-benzamide analogs was designed as inhibitors of B-RAF ^V600E. Medicinal chemistry techniques were employed to explore the SAR for this series and improve selectivity versus P38 and VEGFR2.

Organizational Affiliation

Global Discovery Chemistry/Oncology & Exploratory Chemistry, Novartis Institutes for Biomedical Research, 5300 Chiron Way, Emeryville, CA 94608, United States.

Macromolecule Content

Total Structure Weight: 42.9 kDa
Atom Count: 3,123
Modelled Residue Count: 350
Deposited Residue Count: 369
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	369	Homo sapiens	Mutation(s): 1 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 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
8EN Query on 8EN 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]	~{N}-[3-(2-acetamidoimidazo[1,2-a]pyridin-6-yl)-4-methyl-phenyl]-3-(trifluoromethyl)benzamide C₂₄ H₁₉ F₃ N₄ O₂ MRTHXFZEQBERDI-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
8EN	BindingDB: 5MZ3	IC50: 220 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.15 Å
R-Value Free: 0.197
R-Value Work: 0.165
R-Value Observed: 0.166
Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 45.919	α = 90
b = 85.607	β = 90
c = 127.468	γ = 90

Software Package:

Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
BUSTER	refinement
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-11-15

Deposition Author(s):

Cowan-Jacob, S.W.

Scheufler, C.

Revision History (Full details and data files)

Version 1.0: 2017-11-15
Type: Initial release
Version 1.1: 2017-11-29
Changes: Database references
Version 1.2: 2018-11-07
Changes: Data collection, Source and taxonomy, Structure summary
Version 1.3: 2024-05-08
Changes: Data collection, Database references