9HYP: SMARCA2-vcb-complex with protac P5

Crystal structure of the SMARCA2-vcb-complex with protac P5. Determined by X-ray diffraction at 2.2 Å resolution. Released 22 Oct 2025.

Method: X-ray diffraction
Resolution: 2.2 Å
Organism: Homo sapiens
Chains: 4
Atoms: 3,681
Mol. weight: 56.86 kDa
Ligands: A1IYM
Released: 22 Oct 2025

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

Secondary structure: helices and β-sheets

9HYP contains 26 α-helices and 27 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, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1377-1380	4
α-helix	1381-1395	15
β-strand	1398	1	1
β-strand	1404	1	1
α-helix	1405-1409	5
α-helix	1412-1414	3
α-helix	1419-1424	6
α-helix	1431-1439	9
α-helix	1446-1463	18
α-helix	1465	1
α-helix	1469-1490	22

Chain B: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	2
β-strand	10	1	3
β-strand	12-19	8	2
β-strand	23	1	4
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	2
β-strand	49-50	2	2
β-strand	56	1	4
α-helix	57-60	4
β-strand	68	1	5
β-strand	71	1	5
α-helix	72	1
β-strand	73-79	7	2
β-strand	90	1	3
α-helix	98-100	3
α-helix	101-103	3

Chain C: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	2
β-strand	28-32	5	2
α-helix	33-36	4
α-helix	40-45	6
β-strand	59-61	3	2
α-helix	67-83	17
α-helix	89-92	4
α-helix	100-110	11

Chain D: 6 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	142-144	3
β-strand	147-152	6	6
α-helix	158-169	12
α-helix	172-177	6
α-helix	182-189	8
α-helix	194-210	17

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Probable global transcription activator SNF2L2	A	protein	123	Homo sapiens	P51531 (AlphaFold model)
Elongin-B	B	protein	104	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	C	protein	97	Homo sapiens	Q15369 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	D	protein	162	Homo sapiens	P40337 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9HYP_1 Probable global transcription activator SNF2L2 (chains A)
SMAEKLSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKPVD
FKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQKIAK
EEE

Sequence of entity 2 (B), FASTA

>9HYP_2 Elongin-B (chains B)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Sequence of entity 3 (C), FASTA

>9HYP_3 Elongin-C (chains C)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 4 (D), FASTA

>9HYP_4 von Hippel-Lindau disease tumor suppressor (chains D)
GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Ligands and cofactors

ID	Name	Formula	Copies
A1IYM	(2~{S},4~{R})-~{N}-[[2-[4-[4-(4-bromanyl-7-cyclopentyl-5-oxidanylidene-6~{H}-be…	C54 H65 Br F N8 O6 S	1

Primary citation

Frustration in the protein-protein interface plays a central role in the cooperativity of PROTAC ternary complexes. Ma, N., Bhattacharya, S., Muk, S. et al. Nat Commun (2025) 16:8595-8595. DOI 10.1038/s41467-025-63713-7 · PubMed

Other PDB entries of the same protein (UniProt P51531 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6HAZ 1.31 Å, Crystal structure of the bromodomain of human SMARCA2 in complex with SMARCA-BD ligand
7Z76 1.32 Å, Crystal structure of compound 10 in complex with the bromodomain of human SMARCA2 and…
7Z78 1.32 Å, Crystal structure of compound 4 in complex with the bromodomain of human SMARCA2 and…
5DKC 1.6 Å, Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with PFI-3…
9D11 1.68 Å, Smarca2 Bromodomain in complex with compound 22
5DKH 1.7 Å, Crystal structure of the bromodomain of human BRM (SMARCA2) in complex with a…
9E30 1.71 Å, Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 13
9E31 1.96 Å, Discovery of Potent, Highly Selective and Efficacious SMARCA2 Degraders - Compound 6
4QY4 1.97 Å, Crystal structure of the bromodomain of human SMARCA2
7Z77 1.97 Å, Crystal structure of compound 6 in complex with the bromodomain of human SMARCA2 and…
9QAC 2.07 Å, Crystal structure of the SMARCA2 bromodomain bound to a fragment screening hit
9QAD 2.08 Å, Crystal structure of the SMARCA2 bromodomain bound to a tricyclic pyrimidoindolone…

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