9SFM: Cereblon-DDB1

Name: PDB 9SFM: Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide
Published: 2025-11-19
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: ligase

Crystal structure of Cereblon-DDB1 in complex with SB-405483 and Lenalidomide. Determined by X-ray diffraction at 2.39 Å resolution. Released 19 Nov 2025.

Method: X-ray diffraction
Resolution: 2.39 Å
Organism: Homo sapiens
Chains: 2
Atoms: 12,372
Mol. weight: 173.18 kDa
Ligands: A1CEG, LVY, ZN
Released: 19 Nov 2025

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

Secondary structure: helices and β-sheets

9SFM contains 36 α-helices and 122 β-strands across 2 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: 18 helices, 101 β-strands

Element	Residues	Length	Sheet
β-strand	4-10	7	1
β-strand	17-21	5	2
α-helix	28-29	2
β-strand	30-35	6	2
β-strand	38-44	7	2
β-strand	49-56	8	2
β-strand	61-67	7	3
β-strand	76-81	6	3
β-strand	85-94	10	3
β-strand	97-107	11	3
β-strand	115	1	4
β-strand	121-124	4	4
β-strand	130-136	7	4
β-strand	139-144	6	4
β-strand	155-158	4	4
β-strand	164-169	6	5
α-helix	170	1
β-strand	177-184	8	5
β-strand	187-196	10	5
β-strand	201-204	4	5
β-strand	209	1	5
β-strand	218-221	4	6
β-strand	229-232	4	6
β-strand	237-240	4	6
β-strand	245-248	4	6
α-helix	251-253	3
β-strand	258-263	6	7
β-strand	270-275	6	7
β-strand	279-287	9	7
β-strand	297-307	11	7
β-strand	313-316	4	8
β-strand	321-325	5	8
β-strand	331-336	6	8
α-helix	340-343	4
β-strand	347-353	7	8
β-strand	359-365	7	9
β-strand	374-379	6	9
α-helix	382-384	3
β-strand	386-393	8	9
β-strand	394	1	10
β-strand	396-402	7	11
β-strand	409-413	5	12
β-strand	424-429	6	12
β-strand	432-439	8	12
β-strand	442-446	5	12
β-strand	457-463	7	13
β-strand	467-472	6	13
β-strand	476-480	5	13
β-strand	486-490	5	13
β-strand	500-503	4	14
β-strand	507-512	6	14
β-strand	515-522	8	14
β-strand	525-532	8	14
β-strand	538-542	5	15
β-strand	555-560	6	15
β-strand	568-570	3	15
β-strand	576-578	3	15
α-helix	580-582	3
α-helix	587	1
β-strand	588-596	9	16
β-strand	599-606	8	16
β-strand	610-615	6	16
β-strand	626-630	5	16
β-strand	637-643	7	17
β-strand	646-652	7	17
β-strand	657-659	3	17
β-strand	661-662	2	18
β-strand	665-666	2	18
β-strand	669-670	2	17
β-strand	671	1	10
β-strand	678-682	5	11
β-strand	690-694	5	11
β-strand	699-704	6	11
β-strand	709-716	8	9
β-strand	720-727	8	19
α-helix	728-730	3
β-strand	732-743	12	19
β-strand	749-751	3	19
α-helix	756-758	3
β-strand	762-765	4	19
β-strand	785-795	11	19
β-strand	801-806	6	19
β-strand	811-819	9	20
β-strand	828-835	8	20
β-strand	837	1	21
β-strand	840	1	21
β-strand	846-854	9	20
β-strand	857-866	10	20
β-strand	870-876	7	22
β-strand	879-884	6	22
β-strand	887-893	7	22
β-strand	899-906	8	22
β-strand	913-917	5	23
β-strand	920-924	5	23
β-strand	930-936	7	23
β-strand	941-948	8	23
β-strand	954-961	8	24
β-strand	964-969	6	24
β-strand	973-979	7	24
α-helix	986-989	4
β-strand	991	1	23
β-strand	992-999	8	24
β-strand	1004-1009	6	1
β-strand	1025-1032	8	1
β-strand	1037-1042	6	1
α-helix	1045-1059	15
α-helix	1070-1074	5
β-strand	1076-1077	2	25
β-strand	1082-1083	2	25
β-strand	1086	1	24
β-strand	1088-1090	3	1
α-helix	1091-1095	5
α-helix	1096-1099	4
α-helix	1102-1109	8
β-strand	1113-1115	3	26
β-strand	1121-1123	3	26
α-helix	1124-1125	2
α-helix	1126-1137	12
α-helix	1141-1145	5

Chain B: 18 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	47	1	27
α-helix	53-56	4
α-helix	58-60	3
β-strand	65-66	2	28
α-helix	73-74	2
β-strand	78-83	6	28
β-strand	96-101	6	28
α-helix	104-114	11
β-strand	119-127	9	28
β-strand	132-147	16	28
α-helix	149-151	3
β-strand	154-172	19	28
β-strand	178-184	7	28
α-helix	185-186	2
β-strand	188	1	29
α-helix	190-192	3
α-helix	194-197	4
α-helix	200-203	4
α-helix	209-211	3
α-helix	221-231	11
α-helix	233-237	5
α-helix	242-246	5
α-helix	250-264	15
α-helix	277-287	11
α-helix	292-300	9
β-strand	303	1	29
α-helix	304-317	14
β-strand	320-323	4	30
β-strand	330-333	4	30
β-strand	337	1	31
β-strand	346-350	5	31
β-strand	356-362	7	31
β-strand	368-375	8	31
β-strand	384-391	8	31
β-strand	397-404	8	31
β-strand	410	1	27
β-strand	413-418	6	31
α-helix	419-421	3
β-strand	422-425	4	30

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DNA damage-binding protein 1	A	protein	1148	Homo sapiens	Q16531 (AlphaFold model)
Protein cereblon	B	protein	382	Homo sapiens	Q96SW2 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9SFM_1 DNA damage-binding protein 1 (chains A)
MSYNYVVTAQKPTAVNGCVTGHFTSAEDLNLLIAKNTRLEIYVVTAEGLRPVKEVGMYGK
IAVMELFRPKGESKDLLFILTAKYNACILEYKQSGESIDIITRAHGNVQDRIGRPSETGI
IGIIDPECRMIGLRLYDGLFKVIPLDRDNKELKAFNIRLEELHVIDVKFLYGCQAPTICF
VYQDPQGRHVKTYEVSLREKEFNKGPWKQENVEAEASMVIAVPEPFGGAIIIGQESITYH
NGDKYLAIAPPIIKQSTIVCHNRVDPNGSRYLLGDMEGRLFMLLLEKEEQMDGTVTLKDL
RVELLGETSIAECLTYLDNGVVFVGSRLGDSQLVKLNVDSNEQGSYVVAMETFTNLGPIV
DMCVVDLERQGQGQLVTCSGAFKEGSLRIIRNGIGIHEHASIDLPGIKGLWPLRSDPNRE
TDDTLVLSFVGQTRVLMLNGEEVEETELMGFVDDQQTFFCGNVAHQQLIQITSASVRLVS
QEPKALVSEWKEPQAKNISVASCNSSQVVVAVGRALYYLQIHPQELRQISHTEMEHEVAC
LDITPLGDSNGLSPLCAIGLWTDISARILKLPSFELLHKEMLGGEIIPRSILMTTFESSH
YLLCALGDGALFYFGLNIETGLLSDRKKVTLGTQPTVLRTFRSLSTTNVFACSDRPTVIY
SSNHKLVFSNVNLKEVNYMCPLNSDGYPDSLALANNSTLTIGTIDEIQKLHIRTVPLYES
PRKICYQEVSQCFGVLSSRIEVQDTSGGTTALRPSASTQALSSSVSSSKLFSSSTAPHET
SFGEEVEVHNLLIIDQHTFEVLHAHQFLQNEYALSLVSCKLGKDPNTYFIVGTAMVYPEE
AEPKQGRIVVFQYSDGKLQTVAEKEVKGAVYSMVEFNGKLLASINSTVRLYEWTTEKELR
TECNHYNNIMALYLKTKGDFILVGDLMRSVLLLAYKPMEGNFEEIARDFNPNWMSAVEIL
DDDNFLGAENAFNLFVCQKDSAATTDEERQHLQEVGLFHLGEFVNVFCHGSLVMQNLGET
STPTQGSVLFGTVNGMIGLVTSLSESWYNLLLDMQNRLNKVIKSVGKIEHSFWRSFHTER
KTEPATGFIDGDLIESFLDISRPKMQEVVANLQYDDGSGMKREATADDLIKVVEELTRIH
WSHPQFEK

Sequence of entity 2 (B), FASTA

>9SFM_2 Protein cereblon (chains B)
IINFDTSLPTSHTYLGADMEEFHGRTLHDDDSCQVIPVLPQVMMILIPGQTLPLQLFHPQ
EVSMVRNLIQKDRTFAVLAYSNVQEREAQFGTTAEIYAYREEQDFGIEIVKVKAIGRQRF
KVLELRTQSDGIQQAKVQILPECVLPSTMSAVQLESLNKCQIFPSKPVSREDQCSYKWWQ
KYQKRKFHCANLTSWPRWLYSLYDAETLMDRIKKQLREWDENLKDDSLPSNPIDFSYRVA
ACLPIDDVLRIQLLKIGSAIQRLRCELDIMNKCTSLCCKQCQETEITTKNEIFSLSLCGP
MAAYVNPHGYVHETLTVYKACNLNLIGRPSTEHSWFPGYAWTVAQCKICASHIGWKFTAT
KKDMSPQKFWGLTRSALLPTIP

Ligands and cofactors

ID	Name	Formula	Copies
A1CEG	N-[3-(benzyloxy)pyridin-2-yl]-N'-(4-cyano-2-hydroxyphenyl)urea	C20 H16 N4 O3	1
LVY	S-Lenalidomide	C13 H13 N3 O3	1
ZN	Zinc ion	Zn	1

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

Primary citation

Identification of an allosteric site on the E3 ligase adapter cereblon. Dippon, V.N., Rizvi, Z., Choudhry, A.E. et al. Nature (2026) 651:482-490. DOI 10.1038/s41586-025-09994-w · PubMed

Other PDB entries of the same protein (UniProt Q16531 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9BBG 1.7 Å, Co-crystal structure of human DDB1 bound to fragment UB028671
9EJQ 1.87 Å, Crystal structure of DDB1 in complex with XS381952
9BBI 1.9 Å, Co-crystal structure of human DDB1 bound to fragment UB028669
9BZ0 1.9 Å, Structure of an STK19-containing TC-NER complex
9BBE 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028668
9BBH 2.0 Å, Co-crystal structure of human DDB1 bound to fragment UB028670
9FJX 2.0 Å, Crystal structure of human CRBN-DDB1 in complex with Lenalidomide
9ZXN 2.07 Å, DDB1 delta with compound 26
37MF 2.1 Å, Crystal structure of DDB1 in complex with XS445479
9ZXM 2.19 Å, DDB1 delta with compound 6
8G46 2.2 Å, Cryo-EM structure of DDB1deltaB-DDA1-DCAF16-BRD4(BD2)-MMH2
8ZSW 2.25 Å, Crystal Structure of Human DDB1, a Component of the E3 Ubiquitin Ligase Complex

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