9HNE: Cereblon

Cereblon in complex with DDB1, GSPT1 and Compound-1. Determined by X-ray diffraction at 3.9 Å resolution. Released 22 Oct 2025.

Method: X-ray diffraction
Resolution: 3.9 Å
Organism: Homo sapiens
Chains: 6
Atoms: 26,021
Mol. weight: 391.46 kDa
Ligands: A1IWG, ZN
Released: 22 Oct 2025

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

Secondary structure: helices and β-sheets

9HNE contains 48 α-helices and 307 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.

Chain A: 1 helix, 19 β-strands

Element	Residues	Length	Sheet
β-strand	441-443	3	1
β-strand	457-459	3	2
β-strand	461	1	1
β-strand	469-472	4	1
β-strand	477-483	7	1
β-strand	498-500	3	2
β-strand	503-506	4	1
β-strand	514	1	3
β-strand	516	1	3
β-strand	517-519	3	1
β-strand	530-537	8	4
β-strand	544	1	5
β-strand	548-554	7	4
β-strand	557-571	15	4
β-strand	576-577	2	4
β-strand	585	1	5
β-strand	590-597	8	4
α-helix	610-613	4
β-strand	615-619	5	4
β-strand	622-633	12	4

Chain B: 12 helices, 114 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	6
β-strand	17-21	5	7
β-strand	30-35	6	7
β-strand	38-43	6	7
β-strand	50-56	7	7
β-strand	63-67	5	8
β-strand	76-80	5	8
β-strand	85-92	8	8
β-strand	99-107	9	8
β-strand	115	1	9
β-strand	121-124	4	10
β-strand	130-134	5	10
β-strand	136	1	9
β-strand	139	1	11
β-strand	141-144	4	10
β-strand	151	1	8
β-strand	155	1	10
β-strand	158	1	11
β-strand	164-169	6	12
α-helix	170	1
β-strand	177-184	8	12
β-strand	187-195	9	12
β-strand	202-211	10	12
β-strand	218-221	4	13
β-strand	229-232	4	13
β-strand	237-241	5	13
β-strand	244-248	5	13
α-helix	251-253	3
β-strand	258-263	6	14
β-strand	270-275	6	14
β-strand	278-285	8	14
β-strand	300-306	7	14
β-strand	313-316	4	15
β-strand	321-325	5	15
β-strand	331	1	16
β-strand	332-335	4	15
β-strand	348-349	2	15
β-strand	353	1	16
β-strand	359-365	7	17
β-strand	374-379	6	17
β-strand	386-393	8	17
β-strand	394	1	18
β-strand	396-403	8	19
β-strand	409-413	5	20
β-strand	422	1	21
β-strand	424-428	5	20
β-strand	434-438	5	20
β-strand	443-445	3	20
β-strand	457-459	3	22
β-strand	462-463	2	22
β-strand	467-472	6	22
β-strand	476-480	5	22
β-strand	486-490	5	22
β-strand	500-503	4	23
β-strand	507-512	6	23
β-strand	515-516	2	23
β-strand	519-522	4	23
β-strand	525-528	4	23
β-strand	538-542	5	24
β-strand	555-560	6	24
β-strand	565	1	25
β-strand	566-570	5	24
β-strand	581	1	25
β-strand	588	1	26
β-strand	592-596	5	27
β-strand	599-605	7	27
β-strand	606	1	26
β-strand	610-616	7	27
β-strand	623-630	8	27
β-strand	637-642	6	28
β-strand	647-652	6	28
β-strand	657-660	4	28
β-strand	667-670	4	28
β-strand	671	1	18
β-strand	678-681	4	19
β-strand	684	1	21
β-strand	691-694	4	19
β-strand	698-704	7	19
β-strand	709-716	8	17
β-strand	720-721	2	29
β-strand	725-727	3	29
α-helix	728-730	3
β-strand	732-742	11	29
β-strand	750-751	2	29
β-strand	762	1	29
β-strand	786-795	10	29
β-strand	801-804	4	29
β-strand	811-820	10	30
β-strand	827-835	9	30
β-strand	846-847	2	31
β-strand	848-849	2	30
β-strand	852-854	3	30
β-strand	857-859	3	30
β-strand	865-866	2	31
β-strand	873-876	4	32
β-strand	879-884	6	32
β-strand	887-893	7	32
β-strand	899-906	8	32
β-strand	913-917	5	33
β-strand	920-924	5	33
β-strand	929-936	8	33
β-strand	941-949	9	33
β-strand	954-957	4	34
β-strand	961	1	34
β-strand	964-969	6	34
β-strand	973-978	6	34
β-strand	991	1	33
α-helix	992	1
β-strand	993-999	7	34
β-strand	1007-1008	2	6
β-strand	1025-1030	6	6
β-strand	1037-1042	6	6
α-helix	1043-1044	2
α-helix	1045-1061	17
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1076	1	35
β-strand	1083	1	35
β-strand	1086	1	34
β-strand	1090	1	6
α-helix	1091-1094	4
α-helix	1095-1097	3
α-helix	1102-1108	7
β-strand	1114	1	36
β-strand	1122	1	36
α-helix	1126-1134	9

Chain C: 13 helices, 24 β-strands

Element	Residues	Length	Sheet
α-helix	54-56	3
β-strand	78-83	6	37
β-strand	93	1	37
β-strand	96-101	6	38
α-helix	104-112	9
β-strand	119-124	6	37
β-strand	135-140	6	37
β-strand	143-147	5	38
β-strand	154-160	7	38
β-strand	161-172	12	37
β-strand	178-184	7	37
α-helix	185	1
α-helix	190-192	3
α-helix	228-231	4
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-262	13
α-helix	277-287	11
α-helix	292-300	9
α-helix	304-317	14
β-strand	320-323	4	39
β-strand	330-333	4	39
α-helix	334-336	3
β-strand	337	1	40
β-strand	341	1	41
β-strand	344	1	41
β-strand	347-351	5	40
β-strand	355-362	8	40
β-strand	368	1	42
β-strand	371-375	5	40
β-strand	382	1	40
β-strand	384-390	7	40
β-strand	391	1	42
β-strand	397-404	8	40
β-strand	413-418	6	40
α-helix	419-421	3
β-strand	422-425	4	39

Chain D: 0 helices, 23 β-strands

Element	Residues	Length	Sheet
β-strand	441	1	43
β-strand	457-458	2	44
β-strand	461	1	43
β-strand	464	1	45
β-strand	470-472	3	46
β-strand	477-479	3	46
β-strand	481-485	5	47
β-strand	490-491	2	47
β-strand	494	1	45
β-strand	499-500	2	44
β-strand	501-504	4	47
β-strand	514	1	48
β-strand	516	1	48
β-strand	530-537	8	49
β-strand	544	1	50
β-strand	548-553	6	49
β-strand	558-569	12	49
β-strand	570-571	2	51
β-strand	576-577	2	51
β-strand	585	1	50
β-strand	590-597	8	49
β-strand	615-617	3	49
β-strand	625-629	5	49

Chain E: 9 helices, 102 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	52
β-strand	17-21	5	53
β-strand	30-35	6	53
β-strand	38-43	6	53
β-strand	50-56	7	53
β-strand	61-67	7	54
β-strand	76-81	6	54
β-strand	85-92	8	54
β-strand	99-107	9	54
β-strand	115	1	55
β-strand	121-124	4	55
β-strand	130-136	7	55
β-strand	139-144	6	55
β-strand	156-158	3	55
β-strand	166-169	4	56
β-strand	177-183	7	56
β-strand	188-195	8	56
β-strand	202-204	3	56
β-strand	218-221	4	57
β-strand	229-232	4	57
β-strand	237	1	58
β-strand	238-240	3	57
β-strand	248	1	58
β-strand	258-263	6	59
β-strand	270-275	6	59
β-strand	279-285	7	59
β-strand	300-307	8	59
β-strand	311-318	8	60
β-strand	321-326	6	60
β-strand	331-335	5	60
β-strand	348-353	6	60
β-strand	359-365	7	61
β-strand	374-379	6	61
β-strand	386-393	8	61
β-strand	394	1	62
β-strand	396-403	8	63
β-strand	409-413	5	64
β-strand	424-429	6	64
β-strand	432-438	7	64
β-strand	443-445	3	64
β-strand	457-463	7	65
β-strand	467-472	6	65
β-strand	476-480	5	65
β-strand	486-490	5	65
β-strand	507-508	2	66
β-strand	511-512	2	66
β-strand	515-522	8	66
β-strand	525-533	9	66
β-strand	538-542	5	67
β-strand	555-560	6	67
β-strand	565-570	6	67
β-strand	576-581	6	67
β-strand	588	1	68
β-strand	592-596	5	69
β-strand	599-605	7	69
β-strand	606	1	68
β-strand	610-615	6	69
β-strand	624-630	7	69
β-strand	637-639	3	70
β-strand	642	1	71
β-strand	647	1	71
β-strand	649-652	4	70
β-strand	657-659	3	70
β-strand	669-670	2	70
β-strand	671	1	62
β-strand	678-682	5	63
β-strand	690-694	5	63
β-strand	698-704	7	63
β-strand	709-716	8	61
β-strand	720-727	8	72
α-helix	728-730	3
β-strand	732-742	11	72
β-strand	750-751	2	72
α-helix	756-758	3
β-strand	762	1	72
β-strand	785-795	11	72
β-strand	801-806	6	72
β-strand	811-819	9	73
β-strand	828-835	8	73
β-strand	846-854	9	73
β-strand	857-866	10	73
β-strand	872-876	5	74
β-strand	879-884	6	74
β-strand	887-893	7	74
β-strand	899-906	8	74
β-strand	915-917	3	75
β-strand	920-922	3	75
β-strand	929-934	6	75
β-strand	936	1	76
β-strand	941	1	76
β-strand	944-949	6	75
β-strand	956-957	2	77
β-strand	964	1	77
β-strand	967-969	3	77
β-strand	973-978	6	77
β-strand	991	1	75
β-strand	993-998	6	77
β-strand	1004-1009	6	52
β-strand	1025-1032	8	52
β-strand	1037-1042	6	52
α-helix	1045-1058	14
α-helix	1063-1064	2
α-helix	1070-1073	4
β-strand	1086	1	77
β-strand	1088-1090	3	52
α-helix	1091-1095	5
α-helix	1102-1108	7
β-strand	1113-1114	2	78
β-strand	1122-1123	2	78
α-helix	1126-1128	3
α-helix	1130-1135	6

Chain F: 13 helices, 25 β-strands

Element	Residues	Length	Sheet
β-strand	65-66	2	79
α-helix	73-74	2
β-strand	78-83	6	79
β-strand	93	1	79
β-strand	96-101	6	79
α-helix	104-112	9
β-strand	119-123	5	79
β-strand	135-147	13	79
β-strand	154-161	8	79
β-strand	165-172	8	79
β-strand	178-184	7	79
α-helix	185-186	2
α-helix	193-195	3
α-helix	222-231	10
α-helix	234-237	4
α-helix	244-247	4
α-helix	250-261	12
α-helix	277-284	8
α-helix	292-300	9
α-helix	304-317	14
β-strand	320-323	4	80
β-strand	330-333	4	80
α-helix	334-336	3
β-strand	337	1	81
β-strand	341	1	82
β-strand	344	1	82
β-strand	346-350	5	81
β-strand	356-362	7	81
β-strand	368-375	8	81
β-strand	382	1	83
β-strand	384-385	2	83
β-strand	386-391	6	81
β-strand	397-400	4	81
β-strand	403-404	2	83
β-strand	413	1	83
β-strand	415-418	4	81
α-helix	419-421	3
β-strand	422-425	4	80

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Eukaryotic peptide chain release factor GTP-binding subunit ERF3A	A, D	protein	197	Homo sapiens	P15170 (AlphaFold model)
DNA damage-binding protein 1	B, E	protein	1140	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	C, F	protein	404	Homo sapiens	Q96SW2 (AlphaFold model)

Sequence of entity 1 (A, D), FASTA

>9HNE_1 Eukaryotic peptide chain release factor GTP-binding subunit ERF3A (chains A, D)
GPIRLPIVDKYKDMGTVVLGKLESGSICKGQQLVMMPNKHNVEVLGILSDDVETDTVAPG
ENLKIRLKGIEEEEILPGFILCDPNNLCHSGRTFDAQIVIIEHKSIICPGYNAVLHIHTC
IEEVEITALICLVDKKSGEKSKTRPRFVKQDQVCIARLRTAGTICLETFKDFPQMGRFTL
RDEGKTIAIGKVLKLVP

Sequence of entity 2 (B, E), FASTA

>9HNE_2 DNA damage-binding protein 1 (chains B, E)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH

Sequence of entity 3 (C, F), FASTA

>9HNE_3 Protein cereblon (chains C, F)
SEAKKPNIINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLP
LQLFHPQEVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVK
AIGRQRFKVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQ
CSYKWWQKYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPI
DFSYRVAACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIF
SLSLCGPMAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHI
GWKFTATKKDMSPQKFWGLTRSALLPTIPDTEDEISPDKVILCL

Ligands and cofactors

ID	Name	Formula	Copies
A1IWG	2-[(3~{S})-2,6-bis(oxidanylidene)piperidin-3-yl]-6-fluoranyl-1-oxidanylidene-3~…	C14 H11 F N2 O5	2
ZN	Zinc ion	Zn	2

Primary citation

Targeted degradation of GSPT1 and NEK7 by a molecular glue prodrug for treatment of HCC. Glaza, P., Pluta, R., Odrzywol, K.E. et al. Commun Chem (2025) 8:247-247. DOI 10.1038/s42004-025-01641-9 · PubMed

Other PDB entries of the same protein (UniProt P15170 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3KUI 2.3 Å, Crystal structure of C-terminal domain of PABPC1 in complex with binding region of eRF3a
12BP 2.9 Å, Cryo-EM structure of human DDB1-CRBN-GSPT1 in complex with GT19630
5HXB 3.6 Å, Cereblon in complex with DDB1, CC-885, and GSPT1
6XK9 3.64 Å, Cereblon in complex with DDB1, CC-90009, and GSPT1
5LZT 3.65 Å, Structure of the mammalian ribosomal termination complex with eRF1 and eRF3.
3E1Y 3.8 Å, Crystal structure of human eRF1/eRF3 complex
4D61 9.0 Å, Cryo-EM structures of ribosomal 80S complexes with termination factors and cricket…
3J5Y 9.7 Å, Structure of the mammalian ribosomal pre-termination complex associated with…

Browse structure collections

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