6XDM: Human HDAC2

Structure of human HDAC2 in complex with an aryl ketone inhibitor. Determined by X-ray diffraction at 1.56 Å resolution. Released 29 Jul 2020.

Method: X-ray diffraction
Resolution: 1.56 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,502
Mol. weight: 132.74 kDa
Ligands: V1D, CA, ZN
Released: 29 Jul 2020

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

Secondary structure: helices and β-sheets

6XDM contains 56 α-helices and 50 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: 18 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	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	279-290	12
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, 18 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	85-88	4
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
β-strand	234	1	9
α-helix	235-253	19
β-strand	257-261	5	6
α-helix	264-266	3
β-strand	267	1	10
β-strand	276	1	9
β-strand	277	1	10
α-helix	279-290	12
β-strand	296-299	4	6
α-helix	306-321	16
β-strand	328	1	11
α-helix	329-331	3
α-helix	335-338	4
β-strand	343	1	11
α-helix	357-371	15

Chain C: 19 helices, 16 β-strands

Element	Residues	Length	Sheet
β-strand	12-15	4	12
α-helix	20-22	3
α-helix	34-45	12
α-helix	49-51	3
β-strand	53-55	3	12
α-helix	56-61	6
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	12
β-strand	144	1	13
β-strand	147	1	13
β-strand	149	1	14
β-strand	152	1	14
α-helix	156-164	9
β-strand	171-175	5	12
α-helix	182-187	6
β-strand	194-201	8	12
α-helix	218-220	3
β-strand	224-229	6	12
α-helix	235-253	19
β-strand	257-261	5	12
α-helix	264-266	3
β-strand	267	1	15
β-strand	277	1	15
α-helix	279-290	12
β-strand	296-299	4	12
α-helix	306-320	15
β-strand	328	1	16
α-helix	329-331	3
α-helix	335-338	4
β-strand	343	1	16
α-helix	357-371	15

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

>6XDM_1 Histone deacetylase 2 (chains A, B, C)
MAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKA
TAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVA
GAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHH
GDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQ
IFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLG
GGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYM
EKIKQRLFENLRMLPH

Ligands and cofactors

ID	Name	Formula	Copies
V1D	N-[(1S)-1-[4-(2-fluorophenyl)-1H-imidazol-2-yl]-7,7-dihydroxy-7-(1,2-oxazol-3-y…	C24 H30 F N5 O4	3
CA	Calcium ion	Ca	6
ZN	Zinc ion	Zn	3

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

Primary citation

Selective Class I HDAC Inhibitors Based on Aryl Ketone Zinc Binding Induce HIV-1 Protein for Clearance. Liu, J., Kelly, J., Yu, W. et al. ACS Med Chem Lett (2020) 11:1476-1483. DOI 10.1021/acsmedchemlett.0c00302 · 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…
6XEB 1.5 Å, Structure of human HDAC2 in complex with ketone inhibitor (compound E)
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)
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

About this viewer

MolViewer shows 6XDM 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.