9CMV | pdb_00009cmv

Crystal structure of the KRAS-p110alpha complex in the presence of molecular glue D223

PDB DOI: https://doi.org/10.2210/pdb9CMV/pdb

Classification: ONCOPROTEIN
Organism(s): Homo sapiens
Expression System: Trichoplusia ni, Escherichia coli
Mutation(s): Yes

Deposited: 2024-07-15 Released: 2025-07-23
Deposition Author(s): Czyzyk, D.J., Yan, W., Simanshu, D.K.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.01 Å
R-Value Free:
0.268 (Depositor), 0.267 (DCC)
R-Value Work:
0.231 (Depositor), 0.232 (DCC)
R-Value Observed:
0.234 (Depositor)

Starting Models: 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

Molecular glues that facilitate RAS binding to PI3Kalpha promote glucose uptake without insulin

Czyzyk, D.J., Yan, W., Messing, S., Gillette, W., Esposito, D., Nissley, D.V., McCormick, F., Simanshu, D.K.

(2025) Science

DOI: https://doi.org/10.1126/science.adr9097

Macromolecule Content

Total Structure Weight: 132.7 kDa
Atom Count: 8,446
Modeled Residue Count: 1,059
Deposited Residue Count: 1,135
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Phosphatidylinositol 4,5-bisphosphate 3-kinase catalytic subunit alpha isoform	A	965	Homo sapiens	Mutation(s): 3 Gene Names: PIK3CA EC: 2.7.1.137 (PDB Primary Data), 2.7.1.153 (PDB Primary Data), 2.7.11.1 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P42336 (Homo sapiens) Explore P42336 Go to UniProtKB: P42336
PHAROS: P42336 GTEx: ENSG00000121879
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42336
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
GTPase KRas	B	170	Homo sapiens	Mutation(s): 0 Gene Names: KRAS, KRAS2, RASK2 EC: 3.6.5.2
UniProt & NIH Common Fund Data Resources
Find proteins for P01116 (Homo sapiens) Go to UniProtKB: P01116
PHAROS: P01116 GTEx: ENSG00000133703
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01116-2
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1AZD (Subject of Investigation/LOI) Query on A1AZD Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	tert-butyl [2-(2-{[(2P)-2-{4-[4-(2-amino-2-oxoethyl)-2-fluoroanilino]thieno[2,3-d]pyridazin-7-yl}phenyl]oxy}ethoxy)ethyl]carbamate C₂₉ H₃₂ F N₅ O₅ S NFCHONNVHGPRMI-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
GNP (Subject of Investigation/LOI) Query on GNP Download Ideal Coordinates CCD File SDF format, chain G [auth B] MOL2 format, chain G [auth B] mmCIF format, chain G [auth B]	G [auth B]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain G [auth B] Interactions & Density Focus chain G [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth B]	F [auth A], H [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth B]