8QVU

Crystal Structure of ligand ACBI3 in complex with KRAS G12D C118S GDP and pVHL:ElonginC:ElonginB complex

PDB DOI: https://doi.org/10.2210/pdb8QVU/pdb

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

Deposited: 2023-10-18 Released: 2023-12-06
Deposition Author(s): Wijaya, A.J., Zollman, D., Farnaby, W., Ciulli, A.
Funding Organization(s): Boehringer Ingelheim Fonds (BIF)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.24 Å
R-Value Free: 0.287
R-Value Work: 0.248
R-Value Observed: 0.250

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Targeting cancer with small molecule pan-KRAS degraders

Popow, J., Farnaby, W., Gollner, A., Kofink, C., Fischer, G., Wurm, M., Zollman, D., Wijaya, A., Mischerikow, N., Hasenoehrl, C., Prokofeva, P., Arnhof, H., Arce-Solano, S., Bell, S., Boeck, G., Diers, E., Frost, A., Goodwin-Tindall, J., Karolyi-Oezguer, J., Khan, S., Klawatsch, T., Koegl, M., Kousek, R., Kratochvil, B., Kropatsch, K., Lauber, A., McLennan, R., Olt, S., Peter, D., Petermann, O., Roessler, V., Stolt-Bergner, P., Strack, P., Strauss, E., Trainor, N., Vetma, V., Whitworth, C., Zhong, S., Quant, J., Weinstabl, H., Kuster, B., Ettmayer, P., Ciulli, A.

(2023) Biorxiv

DOI: https://doi.org/10.1101/2023.10.24.563163

Macromolecule Content

Total Structure Weight: 139.88 kDa
Atom Count: 7,887
Modelled Residue Count: 986
Deposited Residue Count: 1,204
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	A [auth H], D	104	Homo sapiens	Mutation(s): 0 Gene Names: ELOB, TCEB2
UniProt & NIH Common Fund Data Resources
Find proteins for Q15370 (Homo sapiens) Explore Q15370 Go to UniProtKB: Q15370
PHAROS: Q15370 GTEx: ENSG00000103363
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15370
Sequence Annotations Expand
Reference Sequence

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Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	B [auth G], E [auth C]	97	Homo sapiens	Mutation(s): 0 Gene Names: ELOC, TCEB1
UniProt & NIH Common Fund Data Resources
Find proteins for Q15369 (Homo sapiens) Explore Q15369 Go to UniProtKB: Q15369
PHAROS: Q15369 GTEx: ENSG00000154582
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q15369
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	C [auth F], F [auth B]	213	Homo sapiens	Mutation(s): 0 Gene Names: VHL
UniProt & NIH Common Fund Data Resources
Find proteins for P40337 (Homo sapiens) Explore P40337 Go to UniProtKB: P40337
PHAROS: P40337 GTEx: ENSG00000134086
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P40337
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform 2B of GTPase KRas	G [auth E], H [auth A]	188	Homo sapiens	Mutation(s): 2 Gene Names: KRAS
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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P01116
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WYL (Subject of Investigation/LOI) Query on WYL Download Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth E] MOL2 format, chain J [auth B] MOL2 format, chain K [auth E]	J [auth B], K [auth E]	(2S,4R)-1-[(2S)-2-[4-[4-[(3S)-4-[4-[5-[(4S)-2-azanyl-3-cyano-4-methyl-6,7-dihydro-5H-1-benzothiophen-4-yl]-1,2,4-oxadiazol-3-yl]pyrimidin-2-yl]-3-methyl-1,4-diazepan-1-yl]butoxy]-1,2,3-triazol-1-yl]-3-methyl-butanoyl]-N-[(1R)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]-2-oxidanyl-ethyl]-4-oxidanyl-pyrrolidine-2-carboxamide C₅₀ H₆₂ N₁₄ O₆ S₂ DQRZNYPHOWVXPQ-YDUPODKQSA-N		Interactions Focus chain J [auth B] Focus chain K [auth E] Interactions & Density Focus chain J [auth B] Focus chain K [auth E]
GDP (Subject of Investigation/LOI) Query on GDP Download Ideal Coordinates CCD File SDF format, chain L [auth E] SDF format, chain N [auth A] MOL2 format, chain L [auth E] MOL2 format, chain N [auth A]	L [auth E], N [auth A]	GUANOSINE-5'-DIPHOSPHATE C₁₀ H₁₅ N₅ O₁₁ P₂ QGWNDRXFNXRZMB-UUOKFMHZSA-N		Interactions Focus chain L [auth E] Focus chain N [auth A] Interactions & Density Focus chain L [auth E] Focus chain N [auth A]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain I [auth B] MOL2 format, chain I [auth B]	I [auth B]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain I [auth B] Interactions & Density Focus chain I [auth B]
MG (Subject of Investigation/LOI) Query on MG Download Ideal Coordinates CCD File SDF format, chain M [auth E] SDF format, chain O [auth A] MOL2 format, chain M [auth E] MOL2 format, chain O [auth A]	M [auth E], O [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain M [auth E] Focus chain O [auth A] Interactions & Density Focus chain M [auth E] Focus chain O [auth A]