6XEB: Human HDAC2

Structure of human HDAC2 in complex with ketone inhibitor (compound E). Determined by X-ray diffraction at 1.5 Å resolution. Released 12 Aug 2020.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,437
Mol. weight: 132.7 kDa
Ligands: ZN, CA, V1P
Released: 12 Aug 2020

Explore 6XEB in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6XEB contains 57 α-helices and 48 β-strands across 3 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: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	1
α-helix	20-22	3
α-helix	34-45	12
α-helix	48-51	4
β-strand	53-55	3	1
α-helix	56-58	3
α-helix	62-65	4
α-helix	71-79	9
α-helix	85-88	4
α-helix	89-94	6
α-helix	107-126	20
β-strand	132-135	4	1
β-strand	144	1	2
β-strand	147	1	2
β-strand	149	1	3
β-strand	152	1	3
α-helix	156-164	9
β-strand	171-175	5	1
α-helix	182-187	6
β-strand	194-201	8	1
α-helix	218-220	3
β-strand	224-229	6	1
α-helix	235-253	19
β-strand	257-261	5	1
α-helix	264-266	3
β-strand	267	1	4
β-strand	277	1	4
α-helix	279-291	13
β-strand	296-299	4	1
α-helix	306-320	15
β-strand	328	1	5
α-helix	329-331	3
α-helix	335-338	4
β-strand	343	1	5
α-helix	357-371	15

Chain B: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	6
α-helix	20-22	3
α-helix	34-45	12
α-helix	48-51	4
β-strand	53-55	3	6
α-helix	56-58	3
α-helix	62-65	4
α-helix	71-79	9
α-helix	85-87	3
α-helix	89-94	6
α-helix	107-126	20
β-strand	132-135	4	6
β-strand	144	1	7
β-strand	147	1	7
β-strand	149	1	8
β-strand	152	1	8
α-helix	156-164	9
β-strand	171-175	5	6
α-helix	182-187	6
β-strand	194-201	8	6
α-helix	218-220	3
β-strand	224-229	6	6
α-helix	235-253	19
β-strand	257-261	5	6
α-helix	264-266	3
β-strand	267	1	9
β-strand	277	1	9
α-helix	279-290	12
β-strand	296-299	4	6
α-helix	306-320	15
β-strand	328	1	10
α-helix	329-331	3
α-helix	335-338	4
β-strand	343	1	10
α-helix	357-371	15

Chain C: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	11
α-helix	20-22	3
α-helix	34-45	12
α-helix	49-51	3
β-strand	53-55	3	11
α-helix	57-61	5
α-helix	62-65	4
α-helix	71-79	9
α-helix	85-88	4
α-helix	89-95	7
α-helix	107-126	20
β-strand	132-135	4	11
β-strand	144	1	12
β-strand	147	1	12
β-strand	149	1	13
β-strand	152	1	13
α-helix	156-164	9
β-strand	171-175	5	11
α-helix	182-188	7
β-strand	194-201	8	11
α-helix	218-220	3
β-strand	224-229	6	11
α-helix	235-253	19
β-strand	257-261	5	11
α-helix	264-266	3
β-strand	267	1	14
β-strand	277	1	14
α-helix	279-290	12
β-strand	296-299	4	11
α-helix	306-320	15
β-strand	328	1	15
α-helix	329-331	3
α-helix	335-338	4
β-strand	343	1	15
α-helix	357-372	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 2	A, B, C	protein	376	Homo sapiens	Q92769 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>6XEB_1 Histone deacetylase 2 (chains A, B, C)
MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKA
TAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVA
GAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHH
GDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQ
IFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLG
GGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYM
EKIKQRLFENLRMLPH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
CA	Calcium ion	Ca	6
V1P	5-{(1S)-7,7-dihydroxy-1-[(1-methylazetidine-3-carbonyl)amino]nonyl}-2-phenyl-1H…	C24 H35 N5 O4	3

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

Primary citation

Development of a selective HDAC inhibitor aimed at reactivating the HIV latent reservoir. Clausen, D.J., Liu, J., Yu, W. et al. Bioorg Med Chem Lett (2020) 30:127367-127367. DOI 10.1016/j.bmcl.2020.127367 · PubMed

Other PDB entries of the same protein (UniProt Q92769 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7KBG 1.26 Å, Structure of Human HDAC2 in complex with a 2-substituted benzamide inhibitor (compound 20)
6WBZ 1.32 Å, Structure of Human HDAC2 in complex with an ethyl ketone inhibitor containing a…
6WBW 1.46 Å, Structure of Human HDAC2 in complex with an ethyl ketone inhibitor
7LTL 1.49 Å, Structure of human HDAC2 in complex with an inhibitor lacking a zinc binding group…
7ZZP 1.52 Å, Structure of HDAC2 complexed with an inhibitory ligand
6WHN 1.54 Å, Histone deacetylases complex with peptide macrocycles
7MOT 1.54 Å, Structure of HDAC2 in complex with an inhibitor (compound 9)
7MOZ 1.54 Å, Structure of HDAC2 in complex with a macrocyclic inhibitor (compound 25)
6XDM 1.56 Å, Structure of human HDAC2 in complex with an aryl ketone inhibitor
7ZZT 1.56 Å, Ligand binding to HDAC2
4LY1 1.57 Å, Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen…
7LTK 1.59 Å, Structure of human HDAC2 in complex with an inhibitor that lacks a zinc binding group…

Browse structure collections

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