9O0U | pdb_00009o0u

Crystal structure of CRAF/MEK1 complex with PLX4720 and CH5126766

PDB DOI: https://doi.org/10.2210/pdb9O0U/pdb

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

Deposited: 2025-04-03 Released: 2025-10-15
Deposition Author(s): Jang, D.M., Eck, M.J.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.91 Å
R-Value Free:
0.264 (Depositor), 0.261 (DCC)
R-Value Work:
0.230 (Depositor), 0.228 (DCC)
R-Value Observed:
0.232 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Characterization and inhibitor sensitivity of ARAF, BRAF, and CRAF kinases

Tkacik, E., Jang, D.M., Boxer, K., Ha, B.H., Eck, M.J.

(2025) J Biological Chem : 110800

DOI: https://doi.org/10.1016/j.jbc.2025.110800

Macromolecule Content

Total Structure Weight: 306.37 kDa
Atom Count: 18,804
Modeled Residue Count: 2,330
Deposited Residue Count: 2,700
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
RAF proto-oncogene serine/threonine-protein kinase	A, C, E, G	280	Homo sapiens	Mutation(s): 2 Gene Names: RAF1, RAF 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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04049
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Dual specificity mitogen-activated protein kinase kinase 1	B, D, F, H	395	Homo sapiens	Mutation(s): 2 Gene Names: MAP2K1, MEK1, PRKMK1 EC: 2.7.12.2
UniProt & NIH Common Fund Data Resources
Find proteins for Q02750 (Homo sapiens) Explore Q02750 Go to UniProtKB: Q02750
PHAROS: Q02750 GTEx: ENSG00000169032
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q02750
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ANP (Subject of Investigation/LOI) Query on ANP Download Ideal Coordinates CCD File SDF format, chain Q [auth H] MOL2 format, chain Q [auth H] mmCIF format, chain Q [auth H]	Q [auth H]	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C₁₀ H₁₇ N₆ O₁₂ P₃ PVKSNHVPLWYQGJ-KQYNXXCUSA-N		Interactions Focus chain Q [auth H] Interactions & Density Focus chain Q [auth H]
CHU (Subject of Investigation/LOI) Query on CHU Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain L [auth D] SDF format, chain N [auth F] SDF format, chain P [auth H] MOL2 format, chain J [auth B] MOL2 format, chain L [auth D] MOL2 format, chain N [auth F] MOL2 format, chain P [auth H] mmCIF format, chain J [auth B] mmCIF format, chain L [auth D] mmCIF format, chain N [auth F] mmCIF format, chain P [auth H]	J [auth B], L [auth D], N [auth F], P [auth H]	N-(3-fluoro-4-{[4-methyl-2-oxo-7-(pyrimidin-2-yloxy)-2H-chromen-3-yl]methyl}pyridin-2-yl)-N'-methylsulfuric diamide C₂₁ H₁₈ F N₅ O₅ S LMMJFBMMJUMSJS-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain L [auth D] Focus chain N [auth F] Focus chain P [auth H] Interactions & Density Focus chain J [auth B] Focus chain L [auth D] Focus chain N [auth F] Focus chain P [auth H]
324 (Subject of Investigation/LOI) Query on 324 Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain K [auth C] SDF format, chain M [auth E] SDF format, chain O [auth G] MOL2 format, chain I [auth A] MOL2 format, chain K [auth C] MOL2 format, chain M [auth E] MOL2 format, chain O [auth G] mmCIF format, chain I [auth A] mmCIF format, chain K [auth C] mmCIF format, chain M [auth E] mmCIF format, chain O [auth G]	I [auth A], K [auth C], M [auth E], O [auth G]	N-{3-[(5-chloro-1H-pyrrolo[2,3-b]pyridin-3-yl)carbonyl]-2,4-difluorophenyl}propane-1-sulfonamide C₁₇ H₁₄ Cl F₂ N₃ O₃ S YZDJQTHVDDOVHR-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth G] Interactions & Density Focus chain I [auth A] Focus chain K [auth C] Focus chain M [auth E] Focus chain O [auth G]