9Y3W: NRas-G12D

Crystal structure of NRas-G12D in complex with GDP and compound 13. Determined by X-ray diffraction at 1.56 Å resolution. Released 25 Feb 2026.

Method: X-ray diffraction
Resolution: 1.56 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,132
Mol. weight: 40.94 kDa
Ligands: CIT, A1CSD, MG, GDP
Released: 25 Feb 2026

Explore 9Y3W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9Y3W contains 12 α-helices and 12 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-57	9	1
α-helix	66-73	8
β-strand	77-83	7	1
α-helix	87-91	5
α-helix	93-103	11
β-strand	111-116	6	1
α-helix	127-137	11
β-strand	141-143	3	1
α-helix	152-167	16

Chain B: 6 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
α-helix	16-25	10
β-strand	37-46	10	1
β-strand	49-57	9	1
α-helix	66-73	8
β-strand	77-83	7	1
α-helix	87-91	5
α-helix	93-104	12
β-strand	111-116	6	1
α-helix	127-137	11
β-strand	141-143	3	1
α-helix	152-168	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
GTPase NRas	A, B	protein	171	Homo sapiens	P01111 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9Y3W_1 GTPase NRas (chains A, B)
GPMTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDT
AGQEEYSAMRDQYMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKS
DLPTRTVDTKQAHELAKSYGIPFIETSAKTRQGVEDAFYTLVREIRQYRMK

Ligands and cofactors

ID	Name	Formula	Copies
CIT	Citric acid	C6 H8 O7	1
A1CSD	(4P)-4-{3-[(1R,5S,6r)-3-azabicyclo[3.1.0]hexan-6-yl]-1-cyclopropyl-7-fluoro-4-(…	C29 H26 F2 N4 O	2
MG	Magnesium ion	Mg	3
GDP	Guanosine-5'-diphosphate	C10 H15 N5 O11 P2	2

Primary citation

Structure-Guided Development of NRAS G12D Inhibitors Based on a 5‐Azaindole Core. Cox, J.B., Nair, V., Mandal, P. et al. ACS Med Chem Lett (2026) 17:425-432. DOI 10.1021/acsmedchemlett.5c00647 · PubMed

Other PDB entries of the same protein (UniProt P01111 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BG8 1.2 Å, Tri-complex of Daraxonrasib (RMC-6236), NRAS Q61R, and CypA
24SR 1.23 Å, Human NRAS WT (GDP-bound) in complex with macrocyclic peptide inhibitor AP6296
7F68 1.24 Å, Crystal structure of N-ras S89D
9BG3 1.33 Å, Tri-complex of Daraxonrasib (RMC-6236), NRAS Q61K, and CypA
6ZIO 1.55 Å, Crystal structure of NRAS (C118S) in complex with GDP
8TBI 1.59 Å, Tricomplex of RMC-7977, NRAS WT, and CypA
9BG0 1.64 Å, Tri-complex of Daraxonrasib (RMC-6236), NRAS WT, and CypA
3CON 1.65 Å, Crystal structure of the human NRAS GTPase bound with GDP
6WGH 1.65 Å, Crystal structure of GDP-bound NRAS with ten residues long internal tandem duplication…
5UHV 1.67 Å, wild-type NRas bound to GppNHp
9Y1Y 1.7 Å, Crystal structure of NRas-G12D in complex with GDP and compound 7
9Y1X 1.72 Å, Crystal structure of NRas-G12D in complex with GDP and IACS-56676

Browse structure collections

About this viewer

MolViewer shows 9Y3W directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.