9DTY | pdb_00009dty

Crystal structure of PRT3789 in complex with the bromodomain of human BRM (SMARCA2) and pVHL:ElonginC:ElonginB

PDB DOI: https://doi.org/10.2210/pdb9DTY/pdb

Classification: TRANSCRIPTION
Organism(s): Homo sapiens
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2024-10-02 Released: 2025-10-01
Deposition Author(s): Dou, Y., Wang, M., Xu, C.
Funding Organization(s): Not funded

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.19 Å
R-Value Free:
0.285 (Depositor), 0.281 (DCC)
R-Value Work:
0.256 (Depositor), 0.255 (DCC)
R-Value Observed:
0.257 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

PRT3789 is a First-in-Human SMARCA2-Selective Degrader that Induces Synthetic Lethality in SMARCA4-Mutated Cancers

Hulse, M., Wang, M., Xu, C., Ito, K.

(2025) Cancer Res

DOI: https://doi.org/10.1158/0008-5472.CAN-25-1141

Macromolecule Content

Total Structure Weight: 561.91 kDa
Atom Count: 36,947
Modeled Residue Count: 4,465
Deposited Residue Count: 4,810
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform Short of Probable global transcription activator SNF2L2	A CA [auth c] E GA [auth g] I A, CA [auth c], E, GA [auth g], I, KA [auth k], M, Q, U, Y	120	Homo sapiens	Mutation(s): 0 Gene Names: SMARCA2, BAF190B, BRM, SNF2A, SNF2L2 EC: 3.6.4
UniProt & NIH Common Fund Data Resources
Find proteins for P51531 (Homo sapiens) Go to UniProtKB: P51531
PHAROS: P51531 GTEx: ENSG00000080503
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P51531-2
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
von Hippel-Lindau disease tumor suppressor	B DA [auth d] F HA [auth h] J B, DA [auth d], F, HA [auth h], J, LA [auth l], N, R, V, Z	161	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: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-C	AA [auth a] C EA [auth e] G IA [auth i] AA [auth a], C, EA [auth e], G, IA [auth i], K, MA [auth m], O, S, W	96	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Elongin-B	BA [auth b] D FA [auth f] H JA [auth j] BA [auth b], D, FA [auth f], H, JA [auth j], L, NA [auth n], P, T, X	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
A1BB4 Query on A1BB4 Download Ideal Coordinates CCD File SDF format, chain AB [auth d] SDF format, chain CB [auth h] SDF format, chain DB [auth k] SDF format, chain OA [auth B] SDF format, chain QA [auth F] SDF format, chain SA [auth J] SDF format, chain TA [auth N] SDF format, chain UA [auth R] SDF format, chain WA [auth V] SDF format, chain YA [auth Z] MOL2 format, chain AB [auth d] MOL2 format, chain CB [auth h] MOL2 format, chain DB [auth k] MOL2 format, chain OA [auth B] MOL2 format, chain QA [auth F] MOL2 format, chain SA [auth J] MOL2 format, chain TA [auth N] MOL2 format, chain UA [auth R] MOL2 format, chain WA [auth V] MOL2 format, chain YA [auth Z] mmCIF format, chain AB [auth d] mmCIF format, chain CB [auth h] mmCIF format, chain DB [auth k] mmCIF format, chain OA [auth B] mmCIF format, chain QA [auth F] mmCIF format, chain SA [auth J] mmCIF format, chain TA [auth N] mmCIF format, chain UA [auth R] mmCIF format, chain WA [auth V] mmCIF format, chain YA [auth Z]	AB [auth d] CB [auth h] DB [auth k] OA [auth B] QA [auth F] AB [auth d], CB [auth h], DB [auth k], OA [auth B], QA [auth F], SA [auth J], TA [auth N], UA [auth R], WA [auth V], YA [auth Z]	(4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-5,6,6a,7,9,10-hexahydro-8H-pyrazino[1',2':4,5]pyrazino[2,3-c]pyridazin-8-yl]pyrrolidin-1-yl}propan-2-yl]oxy}-1,2-oxazol-5-yl)-3-methylbutanoyl]-N-{(1S)-1-[4-(4-methyl-1,3-thiazol-5-yl)phenyl]ethyl}-L-prolinamide C₄₇ H₅₈ N₁₀ O₆ S OSRJAZPHBNGCLU-CMMQWICPSA-N		Interactions Focus chain AB [auth d] Focus chain CB [auth h] Focus chain DB [auth k] Focus chain OA [auth B] Focus chain QA [auth F] Focus chain SA [auth J] Focus chain TA [auth N] Focus chain UA [auth R] Focus chain WA [auth V] Focus chain YA [auth Z] Interactions & Density Focus chain AB [auth d] Focus chain CB [auth h] Focus chain DB [auth k] Focus chain OA [auth B] Focus chain QA [auth F] Focus chain SA [auth J] Focus chain TA [auth N] Focus chain UA [auth R] Focus chain WA [auth V] Focus chain YA [auth Z]
CIT Query on CIT Download Ideal Coordinates CCD File SDF format, chain BB [auth e] SDF format, chain PA [auth C] SDF format, chain VA [auth S] SDF format, chain XA [auth W] SDF format, chain ZA [auth a] MOL2 format, chain BB [auth e] MOL2 format, chain PA [auth C] MOL2 format, chain VA [auth S] MOL2 format, chain XA [auth W] MOL2 format, chain ZA [auth a] mmCIF format, chain BB [auth e] mmCIF format, chain PA [auth C] mmCIF format, chain VA [auth S] mmCIF format, chain XA [auth W] mmCIF format, chain ZA [auth a]	BB [auth e], PA [auth C], VA [auth S], XA [auth W], ZA [auth a]	CITRIC ACID C₆ H₈ O₇ KRKNYBCHXYNGOX-UHFFFAOYSA-N		Interactions Focus chain BB [auth e] Focus chain PA [auth C] Focus chain VA [auth S] Focus chain XA [auth W] Focus chain ZA [auth a] Interactions & Density Focus chain BB [auth e] Focus chain PA [auth C] Focus chain VA [auth S] Focus chain XA [auth W] Focus chain ZA [auth a]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain RA [auth F] MOL2 format, chain RA [auth F] mmCIF format, chain RA [auth F]	RA [auth F]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain RA [auth F] Interactions & Density Focus chain RA [auth F]