7S4E: Ligand ACBi1

Crystal Structure of ligand ACBi1 in complex with bromodomain of human Smarca2 and pVHL:ElonginC:ElonginB complex. Determined by X-ray diffraction at 2.25 Å resolution. Released 5 Oct 2022.

Method: X-ray diffraction
Resolution: 2.25 Å
Organism: Homo sapiens
Chains: 8
Atoms: 7,652
Mol. weight: 114.29 kDa
Ligands: 87A
Released: 5 Oct 2022

Explore 7S4E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7S4E contains 53 α-helices and 58 β-strands across 8 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: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1377-1380	4
α-helix	1381-1396	16
β-strand	1398	1	1
β-strand	1404	1	1
α-helix	1407-1409	3
α-helix	1412-1414	3
α-helix	1419-1424	6
α-helix	1431-1439	9
α-helix	1446-1463	18
α-helix	1469-1488	20

Chain B: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	2
α-helix	83	1
β-strand	84-89	6	3
β-strand	95-97	3	3
β-strand	101	1	3
β-strand	106-112	7	2
β-strand	116-121	6	3
β-strand	127	1	3
β-strand	129-130	2	2
β-strand	133	1	2
β-strand	136	1	3
α-helix	145-146	2
β-strand	147-152	6	2
α-helix	158-169	12
α-helix	172-177	6
α-helix	184-189	6
α-helix	194-206	13

Chains C and G: 5 helices, 3 β-strands

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

Chain D: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	4
β-strand	10	1	5
β-strand	12-19	8	4
β-strand	23	1	6
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	4
β-strand	49-50	2	4
α-helix	51-52	2
β-strand	56	1	6
α-helix	58-60	3
β-strand	68	1	7
β-strand	71	1	7
α-helix	72	1
β-strand	73-79	7	4
β-strand	80-81	2	8
β-strand	84-85	2	8
α-helix	86-88	3
β-strand	90	1	5
α-helix	91-97	7
α-helix	101-103	3

Chain E: 7 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	1381-1396	16
β-strand	1398	1	9
β-strand	1404	1	9
α-helix	1407-1409	3
α-helix	1412-1414	3
α-helix	1419-1424	6
α-helix	1431-1439	9
α-helix	1446-1463	18
α-helix	1469-1489	21

Chain F: 6 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	2
β-strand	84-89	6	10
β-strand	95-97	3	10
β-strand	101	1	10
β-strand	106-112	7	2
β-strand	116-121	6	10
β-strand	127	1	10
β-strand	129-130	2	2
β-strand	133	1	2
β-strand	136	1	10
α-helix	138-141	4
α-helix	145-146	2
β-strand	147-152	6	2
α-helix	158-169	12
α-helix	172-177	6
α-helix	183-189	7
α-helix	194-206	13

Chain H: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	11
β-strand	10	1	12
β-strand	12-19	8	11
β-strand	23	1	13
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	11
β-strand	49-50	2	11
α-helix	51-52	2
β-strand	56	1	13
α-helix	57-60	4
β-strand	68	1	14
β-strand	71	1	14
α-helix	72	1
β-strand	73-79	7	11
β-strand	80-81	2	15
β-strand	84-85	2	15
α-helix	86-88	3
β-strand	90	1	12
α-helix	91-97	7
α-helix	101-103	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Isoform Short of Probable global transcription activator SNF2L2	A, E	protein	125	Homo sapiens	P51531 (AlphaFold model)
von Hippel-Lindau disease tumor suppressor	B, F	protein	162	Homo sapiens	P40337 (AlphaFold model)
Elongin-C	C, G	protein	96	Homo sapiens	Q15369 (AlphaFold model)
Elongin-B	D, H	protein	104	Homo sapiens	Q15370 (AlphaFold model)

Sequence of entity 1 (A, E), FASTA

>7S4E_1 Isoform Short of Probable global transcription activator SNF2L2 (chains A, E)
GSGGAEKLSPNPPKLTKQMNAIIDTVINYKDSSGRQLSEVFIQLPSRKELPEYYELIRKP
VDFKKIKERIRNHKYRSLGDLEKDVMLLCHNAQTFNLEGSQIYEDSIVLQSVFKSARQKI
AKEEE

Sequence of entity 2 (B, F), FASTA

>7S4E_2 von Hippel-Lindau disease tumor suppressor (chains B, F)
GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Sequence of entity 3 (C, G), FASTA

>7S4E_3 Elongin-C (chains C, G)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 4 (D, H), FASTA

>7S4E_4 Elongin-B (chains D, H)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Ligands and cofactors

ID	Name	Formula	Copies
87A	N-(1-fluorocyclopropane-1-carbonyl)-3-methyl-L-valyl-(4R)-N-{[2-{2-[4-({4-[3-am…	C49 H58 F N9 O7 S	2

Water and common crystallization additives (PEG, NA, EDO) are not listed.

Primary citation

Predicting the structural basis of targeted protein degradation by integrating molecular dynamics simulations with structural mass spectrometry. Dixon, T., MacPherson, D., Mostofian, B. et al. Nat Commun (2022) 13:5884-5884. DOI 10.1038/s41467-022-33575-4 · 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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