9GTK | pdb_00009gtk

KRAS in complex with DARPin 784_F5

PDB DOI: https://doi.org/10.2210/pdb9GTK/pdb

Classification: SIGNALING PROTEIN
Organism(s): Homo sapiens, synthetic construct
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-18 Released: 2025-06-25
Deposition Author(s): Kapp, J.N., Verdurmen, W., Schaefer, J.V., Kopra, K., Nagy-Davidescu, G., Richard, E., Nokin, M.J., Ernst, P., Tamaskovic, R., Schwill, M., Degen, R., Scholl, C., Santamaria, D., Plueckthun, A.
Funding Organization(s): Swiss Cancer League

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free:
0.201 (Depositor), 0.209 (DCC)
R-Value Work:
0.171 (Depositor), 0.182 (DCC)
R-Value Observed:
0.172 (Depositor)

Starting Models: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A nucleotide-independent, pan-RAS-targeted DARPin elicits anti-tumor activity in a multimodal manner.

Kapp, J.N., Verdurmen, W.P.R., Schaefer, J.V., Kopra, K., Nagy-Davidescu, G., Richard, E., Nokin, M.J., Ernst, P., Tamaskovic, R., Schwill, M., Degen, R., Scholl, C., Santamaria, D., Pluckthun, A.

(2025) Mol Oncol 19: 3266-3286

PubMed: 40517320 Search on PubMed
DOI: https://doi.org/10.1002/1878-0261.70061
Primary Citation Related Structures:
9GTK

PubMed Abstract:
The KRAS oncoprotein is a frequent tumor driver in lung, pancreatic, and colorectal cancers and has proven to be a challenging pharmaceutical target. The first KRAS-targeted therapeutics are now being tested in clinical trials but the consequences of preferentially targeting the GDP or GTP state of KRAS and the relevance of RAS nanoclustering have remained unclear. Here we report a Designed Ankyrin Repeat Protein (DARPin) that recognizes the RAS switch I/II region with low nm affinity, independently of the nucleotide bound (GDP- or GTP state). This DARPin, termed '784_F5', occupies the effector recognition lobe, resulting in interference with SOS-mediated activation, RAS downstream effector interactions, and KRAS nanoclustering. Consequently, this anti-RAS DARPin potently blocks downstream signaling, leading to a strong reduction in proliferation and anchorage-independent growth in RAS-dependent cell lines. We showed that the expression of '784_F5', the pan-RAS, nucleotide-independent DARPin can lead to tumor regression in a colorectal xenograft model which may hold promise for further investigation and development.

Organizational Affiliation

Department of Biochemistry, University of Zurich, Switzerland.

Macromolecule Content

Total Structure Weight: 125.75 kDa
Atom Count: 8,908
Modeled Residue Count: 1,011
Deposited Residue Count: 1,095
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	A, C, D	195	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) Explore P01116 Go to UniProtKB: P01116
PHAROS: P01116 GTEx: ENSG00000133703
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DARPin 784_F5	B, E [auth H], F [auth I]	170	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GNP (Subject of Investigation/LOI) Query on GNP Download:Ideal Coordinates CCD File SDF format, chain TA [auth D] SDF format, chain T [auth A] SDF format, chain NA [auth C] MOL2 format, chain TA [auth D] MOL2 format, chain T [auth A] MOL2 format, chain NA [auth C] mmCIF format, chain TA [auth D] mmCIF format, chain T [auth A] mmCIF format, chain NA [auth C]	NA [auth C], T [auth A], TA [auth D]	PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER C₁₀ H₁₇ N₆ O₁₃ P₃ UQABYHGXWYXDTK-UUOKFMHZSA-N		Interactions Focus chain NA [auth C] Focus chain T [auth A] Focus chain TA [auth D] Interactions & Density Focus chain NA [auth C] Focus chain T [auth A] Focus chain TA [auth D]
1PE Query on 1PE Download:Ideal Coordinates CCD File SDF format, chain BA [auth B] MOL2 format, chain BA [auth B] mmCIF format, chain BA [auth B]	BA [auth B]	PENTAETHYLENE GLYCOL C₁₀ H₂₂ O₆ JLFNLZLINWHATN-UHFFFAOYSA-N		Interactions Focus chain BA [auth B] Interactions & Density Focus chain BA [auth B]
PGE Query on PGE Download:Ideal Coordinates CCD File SDF format, chain UA [auth D] SDF format, chain WA [auth H] SDF format, chain OA [auth C] SDF format, chain CA [auth B] MOL2 format, chain UA [auth D] MOL2 format, chain WA [auth H] MOL2 format, chain OA [auth C] MOL2 format, chain CA [auth B] mmCIF format, chain UA [auth D] mmCIF format, chain WA [auth H] mmCIF format, chain OA [auth C] mmCIF format, chain CA [auth B]	CA [auth B], OA [auth C], UA [auth D], WA [auth H]	TRIETHYLENE GLYCOL C₆ H₁₄ O₄ ZIBGPFATKBEMQZ-UHFFFAOYSA-N		Interactions Focus chain CA [auth B] Focus chain OA [auth C] Focus chain UA [auth D] Focus chain WA [auth H] Interactions & Density Focus chain CA [auth B] Focus chain OA [auth C] Focus chain UA [auth D] Focus chain WA [auth H]
SRT Query on SRT Download:Ideal Coordinates CCD File SDF format, chain PA [auth C] MOL2 format, chain PA [auth C] mmCIF format, chain PA [auth C]	PA [auth C]	S,R MESO-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-XIXRPRMCSA-N		Interactions Focus chain PA [auth C] Interactions & Density Focus chain PA [auth C]
EDO Query on EDO Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain JA [auth C] SDF format, chain N [auth A] SDF format, chain X [auth B] SDF format, chain XA [auth I] SDF format, chain Z [auth B] SDF format, chain Y [auth B] SDF format, chain W [auth B] SDF format, chain V [auth B] SDF format, chain U [auth B] SDF format, chain RA [auth D] SDF format, chain QA [auth D] SDF format, chain Q [auth A] SDF format, chain P [auth A] SDF format, chain O [auth A] SDF format, chain M [auth A] SDF format, chain LA [auth C] SDF format, chain L [auth A] SDF format, chain KA [auth C] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain IA [auth C] SDF format, chain HA [auth C] SDF format, chain H [auth A] SDF format, chain GA [auth C] SDF format, chain FA [auth C] SDF format, chain EA [auth C] SDF format, chain DA [auth C] SDF format, chain AA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain JA [auth C] MOL2 format, chain N [auth A] MOL2 format, chain X [auth B] MOL2 format, chain XA [auth I] MOL2 format, chain Z [auth B] MOL2 format, chain Y [auth B] MOL2 format, chain W [auth B] MOL2 format, chain V [auth B] MOL2 format, chain U [auth B] MOL2 format, chain RA [auth D] MOL2 format, chain QA [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain P [auth A] MOL2 format, chain O [auth A] MOL2 format, chain M [auth A] MOL2 format, chain LA [auth C] MOL2 format, chain L [auth A] MOL2 format, chain KA [auth C] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain IA [auth C] MOL2 format, chain HA [auth C] MOL2 format, chain H [auth A] MOL2 format, chain GA [auth C] MOL2 format, chain FA [auth C] MOL2 format, chain EA [auth C] MOL2 format, chain DA [auth C] MOL2 format, chain AA [auth B] mmCIF format, chain G [auth A] mmCIF format, chain I [auth A] mmCIF format, chain JA [auth C] mmCIF format, chain N [auth A] mmCIF format, chain X [auth B] mmCIF format, chain XA [auth I] mmCIF format, chain Z [auth B] mmCIF format, chain Y [auth B] mmCIF format, chain W [auth B] mmCIF format, chain V [auth B] mmCIF format, chain U [auth B] mmCIF format, chain RA [auth D] mmCIF format, chain QA [auth D] mmCIF format, chain Q [auth A] mmCIF format, chain P [auth A] mmCIF format, chain O [auth A] mmCIF format, chain M [auth A] mmCIF format, chain LA [auth C] mmCIF format, chain L [auth A] mmCIF format, chain KA [auth C] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain IA [auth C] mmCIF format, chain HA [auth C] mmCIF format, chain H [auth A] mmCIF format, chain GA [auth C] mmCIF format, chain FA [auth C] mmCIF format, chain EA [auth C] mmCIF format, chain DA [auth C] mmCIF format, chain AA [auth B]	AA [auth B] DA [auth C] EA [auth C] FA [auth C] G [auth A] AA [auth B], DA [auth C], EA [auth C], FA [auth C], G [auth A], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], N [auth A], O [auth A], P [auth A], Q [auth A], QA [auth D], RA [auth D], U [auth B], V [auth B], W [auth B], X [auth B], XA [auth I], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain AA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth I] Focus chain Y [auth B] Focus chain Z [auth B] Interactions & Density Focus chain AA [auth B] Focus chain DA [auth C] Focus chain EA [auth C] Focus chain FA [auth C] Focus chain G [auth A] Focus chain GA [auth C] Focus chain H [auth A] Focus chain HA [auth C] Focus chain I [auth A] Focus chain IA [auth C] Focus chain J [auth A] Focus chain JA [auth C] Focus chain K [auth A] Focus chain KA [auth C] Focus chain L [auth A] Focus chain LA [auth C] Focus chain M [auth A] Focus chain N [auth A] Focus chain O [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain QA [auth D] Focus chain RA [auth D] Focus chain U [auth B] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth B] Focus chain XA [auth I] Focus chain Y [auth B] Focus chain Z [auth B]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain R [auth A] SDF format, chain YA [auth I] SDF format, chain VA [auth H] SDF format, chain SA [auth D] SDF format, chain S [auth A] SDF format, chain MA [auth C] MOL2 format, chain R [auth A] MOL2 format, chain YA [auth I] MOL2 format, chain VA [auth H] MOL2 format, chain SA [auth D] MOL2 format, chain S [auth A] MOL2 format, chain MA [auth C] mmCIF format, chain R [auth A] mmCIF format, chain YA [auth I] mmCIF format, chain VA [auth H] mmCIF format, chain SA [auth D] mmCIF format, chain S [auth A] mmCIF format, chain MA [auth C]	MA [auth C] R [auth A] S [auth A] SA [auth D] VA [auth H] MA [auth C], R [auth A], S [auth A], SA [auth D], VA [auth H], YA [auth I]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain MA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth D] Focus chain VA [auth H] Focus chain YA [auth I] Interactions & Density Focus chain MA [auth C] Focus chain R [auth A] Focus chain S [auth A] Focus chain SA [auth D] Focus chain VA [auth H] Focus chain YA [auth I]