7VKG: AF9 YEATS domain

Crystal structure of AF9 YEATS domain in complex with Compound 10. Determined by X-ray diffraction at 1.83 Å resolution. Released 5 Oct 2022.

Method: X-ray diffraction
Resolution: 1.83 Å
Organism: Homo sapiens
Chains: 1
Atoms: 1,213
Mol. weight: 16.89 kDa
Ligands: 7IV
Released: 5 Oct 2022

Explore 7VKG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7VKG contains 4 α-helices and 10 β-strands across 1 chain. 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, 10 β-strands

Element	Residues	Length	Sheet
β-strand	3-15	13	1
β-strand	26-33	8	1
α-helix	40-42	3
β-strand	44-50	7	2
β-strand	59-62	4	2
β-strand	67-73	7	1
β-strand	77-85	9	2
β-strand	93-100	8	2
α-helix	103-104	2
β-strand	105	1	3
β-strand	107	1	3
α-helix	108-109	2
β-strand	110-120	11	1
α-helix	125-133	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protein AF-9	A	protein	138	Homo sapiens	P42568 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>7VKG_1 Protein AF-9 (chains A)
MASSCAVQVKLELGHRAQVRKKPTVEGFTHDWMVFVRGPEHSNIQHFVEKVVFHLHESFP
RPKRVCKDPPYKVEESGYAGFILPIEVYFKNKEEPRKVRFDYDLFLHLEGHPPVNHLRCE
KLTFNNPTEDFRRKLLKA

Ligands and cofactors

ID	Name	Formula	Copies
7IV	~{N}-(4-chlorophenyl)-2-phenylmethoxy-ethanamide	C15 H14 Cl N O2	1

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

Primary citation

Fragment-Based Discovery of AF9 YEATS Domain Inhibitors. Liu, Y., Jin, R., Lu, H. et al. Int J Mol Sci (2022) 23. DOI 10.3390/ijms23073893 · PubMed

Other PDB entries of the same protein (UniProt P42568 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8PJ7 1.26 Å, MLLT3 in complex with compound PFI-6
5YYF 1.9 Å, Crystal structure of AF9 YEATS domain in complex with a peptide inhibitor…
6MIL 1.93 Å, Crystal structure of AF9 YEATS domain in complex with histone H3K9bu
7EIC 1.95 Å, Crystal structure of AF9 YEATS domain in complex with H4K5acK8ac peptide
7EID 2.0 Å, Crystal structure of AF9 YEATS domain in complex with H4K8acK12ac peptide
8TLX 2.1 Å, Crystal structure of MBP and AF9 AHD fusion protein 3AQA in complex with peptidomimetic…
9ARR 2.1 Å, Crystal structure of AF9 YEATS domain in complex with dicrotonylated at K1007 and K1014…
8TLW 2.11 Å, Crystal structure of MBP and AF9 AHD fusion protein 3AQA in complex with peptidomimetic…
6LS6 2.2 Å, Crystal Structure of YEATS domain of AF9 in complex with H3K9bz peptide
7VKH 2.25 Å, Crystal structure of AF9 YEATS domain in complex with hit 2
4TMP 2.3 Å, Crystal structure of AF9 YEATS bound to H3K9ac peptide
9ARO 2.3 Å, Crystal structure of AF9 YEATS domain in complex with acetylated at K1007 MOZ

Browse structure collections

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