9DTX: PRT3789

Crystal structure of PRT3789 in complex with the bromodomain of human BRG1 (SMARCA4) and pVHL:ElonginC:ElonginB. Determined by X-ray diffraction at 2.11 Å resolution. Released 1 Oct 2025.

Method: X-ray diffraction
Resolution: 2.11 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,199
Mol. weight: 58.5 kDa
Ligands: A1BB4
Released: 1 Oct 2025

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

Secondary structure: helices and β-sheets

9DTX contains 30 α-helices and 29 β-strands across 4 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: 9 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	1
β-strand	10	1	2
β-strand	12-19	8	1
β-strand	23	1	3
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	1
β-strand	49-50	2	1
α-helix	51-52	2
β-strand	56	1	3
α-helix	57-60	4
α-helix	64-66	3
β-strand	68	1	4
β-strand	71	1	4
α-helix	72	1
β-strand	73-79	7	1
β-strand	80-81	2	5
β-strand	84-85	2	5
α-helix	86-87	2
β-strand	90	1	2
α-helix	91-98	8
α-helix	101-103	3

Chain B: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	1
β-strand	28-32	5	1
α-helix	33-36	4
α-helix	40-46	7
β-strand	59-61	3	1
α-helix	67-83	17
α-helix	89-94	6
α-helix	97-110	14

Chain C: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	6
α-helix	83	1
β-strand	84-89	6	7
β-strand	95-97	3	7
β-strand	101	1	7
β-strand	106-112	7	6
β-strand	116-121	6	7
β-strand	127	1	7
β-strand	129-130	2	6
β-strand	133	1	6
β-strand	136	1	7
α-helix	145-146	2
β-strand	147-152	6	6
α-helix	158-169	12
α-helix	172-177	6
α-helix	182-189	8
α-helix	194-204	11
α-helix	206-208	3

Chain D: 9 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1451	1
α-helix	1453-1455	3
α-helix	1456-1471	16
β-strand	1473	1	8
β-strand	1480	1	8
α-helix	1481-1485	5
α-helix	1488-1490	3
α-helix	1495-1500	6
α-helix	1507-1515	9
α-helix	1522-1539	18
α-helix	1545-1566	22

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Elongin-B	A	protein	104	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	B	protein	96	Homo sapiens	Q15369 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	C	protein	161	Homo sapiens	P40337 (AlphaFold model)
Transcription activator BRG1	D	protein	138	Homo sapiens	P51532 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9DTX_1 Elongin-B (chains A)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 2 (B), FASTA

>9DTX_2 Elongin-C (chains B)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (C), FASTA

>9DTX_3 von Hippel-Lindau disease tumor suppressor (chains C)
GMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSY
RGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKP
ENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Sequence of entity 4 (D), FASTA

>9DTX_4 Transcription activator BRG1 (chains D)
GGLNDIFEAQKIEWHEAEKLSPNPPNLTKKMKKIVDAVIKYKDSSSGRQLSEVFIQLPSR
KELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLEKDVMLLCQNAQTFNLEGSLIYEDSI
VLQSVFTSVRQKIEKEDD

Ligands and cofactors

ID	Name	Formula	Copies
A1BB4	(4R)-4-hydroxy-1-[(2R)-2-(3-{[(2S)-1-{(3R)-3-[(2M,6aS,11S)-2-(2-hydroxyphenyl)-…	C47 H58 N10 O6 S	1

Water and common crystallization additives (CL, EDO, GOL) are not listed.

Primary citation

PRT3789 Is a First-in-Human SMARCA2-Selective Degrader That Induces Synthetic Lethality in SMARCA4-Mutated Cancers. Hulse, M., Wang, M., Xu, C. et al. Cancer Res (2026) 86:213-235. DOI 10.1158/0008-5472.CAN-25-1141 · PubMed

Other PDB entries of the same protein (UniProt Q15370 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7Z76 1.32 Å, Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and…
9GIO 1.49 Å, Crystal structure of the VHL-EloC-EloB complex with a covalent compound bound to C77 of…
7JTO 1.7 Å, Crystal structure of Protac MS33 in complex with the WD repeat-containing protein 5 and…
8BDS 1.72 Å, Ternary complex between VCB, BRD4-BD1 and PROTAC 48
4AJY 1.73 Å, von Hippel-Lindau protein-ElonginB-ElonginC complex, bound to Hif1- alpha peptide
6GMR 1.75 Å, pVHL:EloB:EloC in complex with (4-(1H-pyrrol-1-yl)phenyl)methanol
6HR2 1.76 Å, Crystal structure of PROTAC 2 in complex with the bromodomain of human SMARCA4 and…
7ZLM 1.79 Å, Crystal structure of SOCS2:ElonginB:ElonginC in complex with compound MN551
6I7Q 1.8 Å, Structure of pVHL-elongin B-elongin C (VCB) in complex with hydroxylated-HIF-2alpha…
8BB3 1.8 Å, Structure of human WDR5 and pVHL:ElonginC:ElonginB bound to PROTAC with PEG linker…
6GFX 1.83 Å, pVHL:EloB:EloC in complex with modified HIF-1a CODD peptide containing…
1LM8 1.85 Å, Structure of a HIF-1a-pVHL-ElonginB-ElonginC Complex

Browse structure collections

About this viewer

MolViewer shows 9DTX 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.