8UWP: SETDB1 Tudor domain

Crystal structure of SETDB1 Tudor domain in complex with MR46747. Determined by X-ray diffraction at 1.77 Å resolution. Released 22 Nov 2023.

Method: X-ray diffraction
Resolution: 1.77 Å
Organism: Homo sapiens
Chains: 2
Atoms: 3,851
Mol. weight: 54.75 kDa
Ligands: XRU
Released: 22 Nov 2023

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

Secondary structure: helices and β-sheets

8UWP contains 14 α-helices and 38 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: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	5-6	2	2
β-strand	9-10	2	2
β-strand	14-18	5	1
β-strand	24-35	12	1
β-strand	38-45	8	1
β-strand	50-53	4	1
α-helix	55-57	3
β-strand	58-60	3	1
α-helix	63-65	3
α-helix	66-68	3
β-strand	74-80	7	3
β-strand	85-94	10	3
β-strand	104-108	5	3
β-strand	113-116	4	3
α-helix	118-120	3
β-strand	121-123	3	3
β-strand	124	1	1
α-helix	131-134	4
α-helix	138-150	13
β-strand	164-169	6	4
β-strand	172-182	11	4
β-strand	185-190	6	4
β-strand	195-200	6	4
β-strand	206	1	4
α-helix	207-211	5

Chain B: 7 helices, 19 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	5
β-strand	5-6	2	6
β-strand	9-10	2	6
β-strand	14-18	5	5
β-strand	24-35	12	5
β-strand	38-45	8	5
β-strand	50-53	4	5
α-helix	55-57	3
β-strand	58-60	3	5
α-helix	63-65	3
α-helix	66-68	3
β-strand	74-80	7	5
β-strand	85-94	10	5
β-strand	104-108	5	5
β-strand	113-116	4	5
α-helix	118-120	3
β-strand	121-124	4	5
α-helix	131-134	4
β-strand	137	1	1
α-helix	138-150	13
β-strand	164-169	6	7
β-strand	172-182	11	7
β-strand	185-190	6	7
β-strand	195-200	6	7
β-strand	206	1	7
α-helix	207-211	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone-lysine N-methyltransferase SETDB1	A, B	protein	225	Homo sapiens	Q15047 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8UWP_1 Histone-lysine N-methyltransferase SETDB1 (chains A, B)
MHHHHHHSSGRENLYFQGDLIVSMRILGKKRTKTWHKGTLIAIQTVGPGKKYKVKFDNKG
KSLLSGNHIAYDYHPPADKLYVGSRVVAKYKDGNQVWLYAGIVAETPNVKNKLRFLIFFD
DGYASYVTQSELYPICRPLKKTWEDIEDISCRDFIEEYVTAYPNRPMVLLKSGQLIKTEW
EGTWWKSRVEEVDGSLVRILFLDDKRCEWIYRGSTRLEPMFSMKT

Ligands and cofactors

ID	Name	Formula	Copies
XRU	(3S)-N-(4-chloro-3-{[2-(diethylamino)ethyl]carbamoyl}phenyl)-3-(diethylamino)py…	C22 H36 Cl N5 O2	2

Water and common crystallization additives (SO4, EDO, UNX) are not listed.

Primary citation

A Target Class Ligandability Evaluation of WD40 Repeat-Containing Proteins. Ackloo, S., Li, F., Szewczyk, M. et al. J Med Chem (2025) 68:1092-1112. DOI 10.1021/acs.jmedchem.4c02010 · PubMed

Other PDB entries of the same protein (UniProt Q15047 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6BHD 1.25 Å, Crystal structure of SETDB1 with a modified H3 peptide
9CUX 1.27 Å, Crystal Structure of SETDB1 Tudor domain in complex with UNC100016
6BHE 1.35 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHI 1.4 Å, Crystal structure of SETDB1 with a modified H3 peptide
6BHG 1.45 Å, Crystal structure of SETDB1 with a modified H3 peptide
5KCO 1.47 Å, SETDB1 in complex with an early stage, low affinity fragment candidate modelled at…
9CUW 1.53 Å, Crystal Structure of SETDB1 Tudor domain in complex with UNC100013
5KE2 1.56 Å, Crystal structure of SETDB1 Tudor domain in complex with inhibitor XST06472A
5QT1 1.58 Å, PanDDA analysis group deposition -- Partial occupancy interpretation of PanDDA event…
5QT2 1.59 Å, PanDDA analysis group deposition -- Partial occupancy interpretation of PanDDA event…
4X3S 1.6 Å, Crystal structure of chromobox homology 7 (CBX7) with SETDB1-1170me3 Peptide
7CD9 1.6 Å, Crystal Structure of SETDB1 tudor domain in complexed with Compound 6

Browse structure collections

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