8DKB: Human YEATS4

Crystal Structure of human YEATS4 in complex with Pfizer small molecule compound 3b. Determined by X-ray diffraction at 2.58 Å resolution. Released 11 Jan 2023.

Method: X-ray diffraction
Resolution: 2.58 Å
Organism: Homo sapiens
Chains: 8
Atoms: 8,996
Mol. weight: 149.15 kDa
Ligands: SJI
Released: 11 Jan 2023

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

Secondary structure: helices and β-sheets

8DKB contains 34 α-helices and 64 β-strands across 8 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: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	22-33	12	1
β-strand	45-53	9	1
α-helix	59-61	3
β-strand	63-69	7	2
β-strand	78-81	4	2
β-strand	86-92	7	1
β-strand	97-104	8	2
α-helix	110-111	2
β-strand	112-117	6	2
α-helix	122-123	2
α-helix	124-128	5
β-strand	134-143	10	1

Chain B: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	21-33	13	3
β-strand	45-53	9	3
α-helix	59-61	3
β-strand	63-69	7	4
β-strand	78-81	4	4
β-strand	86-92	7	3
β-strand	97-104	8	4
α-helix	110-111	2
β-strand	112-117	6	4
α-helix	121-123	3
α-helix	124-128	5
β-strand	133-144	12	3

Chain C: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	21-33	13	5
β-strand	45-53	9	5
α-helix	59-61	3
β-strand	63-69	7	6
β-strand	78-81	4	6
β-strand	86-92	7	5
β-strand	97-104	8	6
α-helix	110-111	2
β-strand	112-117	6	6
α-helix	122-123	2
α-helix	124-128	5
β-strand	133-144	12	5

Chains D and E: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	22-33	12	7
β-strand	45-53	9	7
α-helix	59-61	3
β-strand	63-69	7	8
β-strand	78-81	4	8
β-strand	86-92	7	7
β-strand	97-104	8	8
α-helix	110-111	2
β-strand	112-117	6	8
α-helix	122-123	2
α-helix	124-128	5
β-strand	133-143	11	7

Chain F: 4 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	22-33	12	11
β-strand	45-53	9	11
α-helix	59-61	3
β-strand	63-69	7	12
β-strand	78-81	4	12
β-strand	86-92	7	11
β-strand	97-104	8	12
α-helix	110-111	2
β-strand	112-117	6	12
α-helix	122-123	2
α-helix	124-127	4
β-strand	133-143	11	11

Chain G: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	22-38	17	13
β-strand	43-53	11	13
α-helix	59-61	3
β-strand	63-69	7	14
α-helix	72-74	3
β-strand	78-81	4	14
β-strand	86-92	7	13
β-strand	97-104	8	14
α-helix	110-111	2
β-strand	112-117	6	14
α-helix	122-123	2
α-helix	124-128	5
β-strand	133-143	11	13

Chain H: 5 helices, 8 β-strands

Element	Residues	Length	Sheet
β-strand	22-33	12	15
β-strand	45-53	9	15
α-helix	59-61	3
β-strand	63-69	7	16
β-strand	78-81	4	16
β-strand	86-92	7	15
β-strand	97-104	8	16
α-helix	110-111	2
β-strand	112-117	6	16
α-helix	118-119	2
α-helix	122-123	2
α-helix	124-128	5
β-strand	133-143	11	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
YEATS domain-containing protein 4	A, B, C, D, E, F, G, H	protein	155	Homo sapiens	O95619 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>8DKB_1 YEATS domain-containing protein 4 (chains A, B, C, D, E, F, G, H)
MFKRMAEFGPDSGGRVKGVTIVKPIVYGNVARYFGKKREEDGHTHQWTVYVKPYRNEDMS
AYVKKIQFKLHESYGNPLRVVTKPPYEITETGWGEFEIIIKIFFIDPNERPVTLYHLLKL
FQSDTNAMLGKKTVVSEFYDEMIFQDPTAHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
SJI	N-ethyl-1-{(3S,4S)-1-[(1-hydroxycyclohexyl)methyl]-3-methylpiperidin-4-yl}-2-me…	C24 H36 N4 O2	8

Primary citation

Discovery of High-Affinity Small-Molecule Binders of the Epigenetic Reader YEATS4. Londregan, A.T., Aitmakhanova, K., Bennett, J. et al. J Med Chem (2023) 66:460-472. DOI 10.1021/acs.jmedchem.2c01421 · PubMed

Other PDB entries of the same protein (UniProt O95619 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8IJ0 1.52 Å, Crystal structure of GAS41 YEATS domain in complex with H3K9ac peptide
7EIF 1.58 Å, Crystal structure of GAS41 YEATS domain
5R68 1.64 Å, XChem group deposition -- Crystal Structure of human YEATS4 in complex with FM000199e
9X8S 1.7 Å, Crystal structure of the human GAS41 YEATS domain in complex with an acetylated YFV…
5R69 1.83 Å, XChem group deposition -- Crystal Structure of human YEATS4 in complex with XS038644e
5VNA 2.1 Å, Crystal structure of human YEATS domain
8IIZ 2.1 Å, Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K27ac peptide
7JFY 2.1 Å, GAS41 YEATS domain in complex with 5
5XTZ 2.1 Å, Crystal structure of GAS41 YEATS bound to H3K27ac peptide
8IIY 2.15 Å, Crystal structure of MBP fused GAS41 YEATS domain in complex with H3K14ac peptide
8I60 2.3 Å, Crystal structure of GAS41 YEATS domain in complex with histone H3K27cr
9O4Y 2.3 Å, GAS41 YEATS domain in complex with DLG-1

Browse structure collections

About this viewer

MolViewer shows 8DKB directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.