8VL9: EloBC-VHL-CDO1 complex

Crystal structure of EloBC-VHL-CDO1 complex bound to compound 8 molecular glue. Determined by X-ray diffraction at 2.5 Å resolution. Released 13 Mar 2024.

Method: X-ray diffraction
Resolution: 2.5 Å
Organism: Homo sapiens
Chains: 4
Atoms: 4,466
Mol. weight: 66.5 kDa
Ligands: A1ACI, CIT, FE2
Released: 13 Mar 2024

Explore 8VL9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8VL9 contains 32 α-helices and 41 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: 7 helices, 11 β-strands

Element	Residues	Length	Sheet
β-strand	71-79	9	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	1	2
β-strand	129-130	2	1
β-strand	133	1	1
β-strand	136	1	2
α-helix	142-144	3
α-helix	145-146	2
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

Chain B: 9 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	80-81	2	7
β-strand	84-85	2	7
α-helix	86-88	3
β-strand	90	1	4
α-helix	91-94	4
α-helix	96-100	5
α-helix	101-103	3

Chain C: 6 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
α-helix	52-53	2
β-strand	59-61	3	3
α-helix	67-83	17
α-helix	97-99	3
α-helix	100-110	11

Chain D: 10 helices, 14 β-strands

Element	Residues	Length	Sheet
α-helix	12-22	11
α-helix	30-39	10
α-helix	41-42	2
α-helix	44-47	4
α-helix	48-50	3
β-strand	59-64	6	8
α-helix	66-68	3
β-strand	71-77	7	8
β-strand	82	1	9
α-helix	83-84	2
β-strand	85-86	2	9
β-strand	92-99	8	8
β-strand	102-107	6	9
α-helix	108-111	4
α-helix	116-118	3
β-strand	119-125	7	9
α-helix	126	1
β-strand	130-133	4	8
β-strand	139-143	5	9
β-strand	151-158	8	8
β-strand	163-167	5	9
β-strand	174-178	5	9
β-strand	183-184	2	8
β-strand	187-188	2	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
von Hippel-Lindau disease tumor suppressor	A	protein	162	Homo sapiens	P40337 (AlphaFold model)
Elongin-B	B	protein	118	Homo sapiens	Q15370 (AlphaFold model)
Elongin-C	C	protein	96	Homo sapiens	Q15369 (AlphaFold model)
Cysteine dioxygenase type 1	D	protein	201	Homo sapiens	Q16878 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8VL9_1 von Hippel-Lindau disease tumor suppressor (chains A)
GPMEAGRPRPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHS
YRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVK
PENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQRMGD

Sequence of entity 2 (B), FASTA

>8VL9_2 Elongin-B (chains B)
MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGEC
GFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMKPQDSGSSANEQAVQ

Sequence of entity 3 (C), FASTA

>8VL9_3 Elongin-C (chains C)
MYVKLISSDGHEFIVKREHALTSGTIKAMLSGPGQFAENETNEVNFREIPSHVLSKVCMY
FTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC

Sequence of entity 4 (D), FASTA

>8VL9_4 Cysteine dioxygenase type 1 (chains D)
GMEQTEVLKPRTLADLIRILHQLFAGDEVNVEEVQAIMEAYESDPTEWAMYAKFDQYRYT
RNLVDQGNGKFNLMILCWGEGHGSSIHDHTNSHCFLKMLQGNLKETLFAWPDKKSNEMVK
KSERVLRENQCAYINDSIGLHRVENISHTEPAVSLHLYSPPFDTCHAFDQRTGHKNKVTM
TFHSKFGIRTPNATSGSLENN

Ligands and cofactors

ID	Name	Formula	Copies
A1ACI	N-acetyl-3-methyl-L-valyl-(4R)-4-hydroxy-N-{[(4P)-4-(1H-pyrazol-3-yl)naphthalen…	C27 H33 N5 O4	1
CIT	Citric acid	C6 H8 O7	1
FE2	FE (II) ion	Fe	1

Primary citation

A small-molecule VHL molecular glue degrader for cysteine dioxygenase 1. Tutter, A., Buckley, D., Golosov, A.A. et al. Nat Chem Biol (2025) 21:1688-1696. DOI 10.1038/s41589-025-01936-x · 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

Browse structure collections

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