8JNB | pdb_00008jnb

CRAF ras-binding domain chimera, ligand complex

PDB DOI: https://doi.org/10.2210/pdb8JNB/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2023-06-06 Released: 2024-06-19
Deposition Author(s): Kawamura, T., Kumasaka, T.
Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Science and Technology

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free:
0.242 (Depositor), 0.243 (DCC)
R-Value Work:
0.204 (Depositor), 0.208 (DCC)
R-Value Observed:
0.206 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 8JNB

Ligand Structure Quality Assessment

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

Literature

Small-molecule RAS/RAF-binding Inhibitors Allosterically Disrupt RAF Conformation and Exert Efficacy Against Broad-spectrum RAS-driven Cancers

Yoshikawa, Y., Makino, Y., Kubota, H., Kawamura, T., Matsumoto, S., Yuki, H., Shibaike, A., Okamura, M., Okada, T., Kataoka, T., Honma, T., Kumasaka, T., Koyama, H., Shima, F.

To be published.

Macromolecule Content

Total Structure Weight: 10.89 kDa
Atom Count: 738
Modeled Residue Count: 81
Deposited Residue Count: 94
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAF proto-oncogene serine/threonine-protein kinase, CRaf	A [auth B]	94	Homo sapiens	Mutation(s): 4 Gene Names: RAF1, RAF, BRAF, BRAF1, RAFB1 EC: 2.7.11.1
UniProt & NIH Common Fund Data Resources
Find proteins for P04049 (Homo sapiens) Explore P04049 Go to UniProtKB: P04049
PHAROS: P04049 GTEx: ENSG00000132155
Find proteins for P15056 (Homo sapiens) Explore P15056 Go to UniProtKB: P15056
PHAROS: P15056 GTEx: ENSG00000157764
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Groups	P15056 P04049
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
USX (Subject of Investigation/LOI) Query on USX Download:Ideal Coordinates CCD File SDF format, chain B MOL2 format, chain B mmCIF format, chain B	B	2-[4-[[(2S)-1-ethanoyl-3-oxidanylidene-2H-indol-2-yl]methyl]-2-methoxy-phenoxy]ethanamide C₂₀ H₂₀ N₂ O₅ DUXGCVPXJWCVOO-INIZCTEOSA-N		Interactions Focus chain B Interactions & Density Focus chain B

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.62 Å
R-Value Free: 0.242 (Depositor), 0.243 (DCC)
R-Value Work: 0.204 (Depositor), 0.208 (DCC)
R-Value Observed: 0.206 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 65.019	α = 90
b = 69.775	β = 90
c = 39.746	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing
Coot	model building

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2024-06-19

Deposition Author(s):

Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	17nk0101309h0003
Japan Science and Technology	Japan	22-20103170

Revision History (Full details and data files)

Version 1.0: 2024-06-19
Type: Initial release
Version 1.1: 2024-11-06
Changes: Structure summary

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.