8P0F: VCB complex with compound 1

Crystal structure of the VCB complex with compound 1. Determined by X-ray diffraction at 1.98 Å resolution. Released 31 May 2023.

Method: X-ray diffraction
Resolution: 1.98 Å
Organism: Homo sapiens
Chains: 6
Atoms: 5,817
Mol. weight: 83.73 kDa
Ligands: WBN
Released: 31 May 2023

Explore 8P0F in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8P0F contains 40 α-helices and 54 β-strands across 6 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.

Chains A and D: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-78	8	1
α-helix	83	1
β-strand	84-89	6	2
β-strand	95-97	3	2
β-strand	101	1	2
β-strand	106-112	7	1
β-strand	116-121	6	2
β-strand	127-128	2	2
β-strand	129-130	2	1
β-strand	133	1	1
β-strand	136	1	2
α-helix	142-144	3
α-helix	146	1
β-strand	147-152	6	1
α-helix	158-169	12
α-helix	172-177	6
α-helix	182-189	8
α-helix	194-206	13

Chains B and E: 5 helices, 3 β-strands

Element	Residues	Length	Sheet
β-strand	18-22	5	3
β-strand	28-32	5	3
α-helix	33-36	4
α-helix	40-47	8
β-strand	59-61	3	3
α-helix	67-83	17
α-helix	89-92	4
α-helix	100-110	11

Chain C: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	3
β-strand	10	1	4
β-strand	12-19	8	3
β-strand	23	1	5
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	3
β-strand	49-50	2	3
α-helix	51-52	2
β-strand	56	1	5
α-helix	57-60	4
β-strand	68	1	6
β-strand	71	1	6
α-helix	72	1
β-strand	73-79	7	3
β-strand	80	1	7
β-strand	85	1	7
α-helix	86-88	3
β-strand	90	1	4
α-helix	91-96	6
α-helix	98-100	3

Chain F: 8 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	2-9	8	10
β-strand	10	1	11
β-strand	12-19	8	10
β-strand	23	1	12
α-helix	24-35	12
α-helix	39-41	3
β-strand	42-46	5	10
β-strand	49-50	2	10
α-helix	51-52	2
β-strand	56	1	12
α-helix	58-60	3
β-strand	68	1	13
β-strand	71	1	13
α-helix	72	1
β-strand	73-79	7	10
β-strand	80	1	14
β-strand	85	1	14
α-helix	86-88	3
β-strand	90	1	11
α-helix	91-96	6
α-helix	98-100	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
von Hippel-Lindau disease tumor suppressor	A, D	protein	162	Homo sapiens	P40337 (AlphaFold model)
Elongin-C	B, E	protein	97	Homo sapiens	Q15369 (AlphaFold model)
Elongin-B	C, F	protein	104	Homo sapiens	Q15370 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>8P0F_1 von Hippel-Lindau disease tumor suppressor (chains A, D)
GSMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Sequence of entity 2 (B, E), FASTA

>8P0F_2 Elongin-C (chains B, E)
MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCM
YFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 3 (C, F), FASTA

>8P0F_3 Elongin-B (chains C, F)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK

Ligands and cofactors

ID	Name	Formula	Copies
WBN	(3~{R},5~{R})-~{N}-[[4-(4-methyl-1,3-thiazol-5-yl)phenyl]methyl]-5-oxidanyl-2-o…	C22 H22 N4 O3 S	2

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

Primary citation

Drugit: crowd-sourcing molecular design of non-peptidic VHL binders. Scott, T., Smethurst, C.A.P., Westermaier, Y. et al. Nat Commun (2025) 16:3548-3548. DOI 10.1038/s41467-025-58406-0 · PubMed

Other PDB entries of the same protein (UniProt P40337 (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…
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
6ZHC 1.92 Å, PROTAC6 mediated complex of VHL:EloB:EloC and Bcl-xL

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