4LY1: Human HDAC2

Structure of Human HDAC2 in complex with inhibitor 4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide. Determined by X-ray diffraction at 1.57 Å resolution. Released 21 Aug 2013.

Method: X-ray diffraction
Resolution: 1.57 Å
Organism: Homo sapiens
Chains: 3
Atoms: 10,080
Mol. weight: 130.3 kDa
Ligands: ZN, CA, 20Y, NHE
Released: 21 Aug 2013

Explore 4LY1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4LY1 contains 57 α-helices and 52 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	16-19	4	1
α-helix	24-26	3
α-helix	38-49	12
α-helix	52-55	4
β-strand	57-59	3	1
α-helix	60-62	3
α-helix	66-69	4
α-helix	75-83	9
α-helix	89-92	4
α-helix	93-99	7
α-helix	111-130	20
β-strand	136-139	4	1
β-strand	148	1	2
β-strand	151	1	2
β-strand	153	1	3
β-strand	156	1	3
α-helix	160-168	9
β-strand	175-179	5	1
α-helix	186-191	6
β-strand	198-205	8	1
α-helix	222-224	3
β-strand	228-233	6	1
α-helix	239-257	19
β-strand	261-265	5	1
α-helix	268-270	3
β-strand	271	1	4
β-strand	281	1	4
α-helix	283-295	13
β-strand	300-303	4	1
α-helix	310-324	15
β-strand	332	1	5
α-helix	333-335	3
α-helix	339-342	4
β-strand	347	1	5
α-helix	361-375	15

Chain B: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	16-19	4	6
α-helix	24-26	3
α-helix	38-49	12
α-helix	52-55	4
β-strand	57-59	3	6
α-helix	60-62	3
α-helix	66-69	4
α-helix	75-83	9
α-helix	86-88	3
α-helix	93-99	7
α-helix	111-130	20
β-strand	136-139	4	6
β-strand	148	1	7
β-strand	151	1	7
β-strand	153	1	8
β-strand	156	1	8
α-helix	160-168	9
β-strand	175-179	5	6
α-helix	186-191	6
β-strand	198-205	8	6
α-helix	222-224	3
β-strand	228-233	6	6
β-strand	238	1	9
α-helix	239-257	19
β-strand	261-265	5	6
α-helix	268-270	3
β-strand	271	1	10
β-strand	280	1	9
β-strand	281	1	10
α-helix	283-294	12
β-strand	300-303	4	6
α-helix	310-324	15
β-strand	332	1	11
α-helix	333-335	3
α-helix	339-342	4
β-strand	347	1	11
α-helix	361-375	15

Chain C: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	16-19	4	12
α-helix	24-26	3
α-helix	38-49	12
α-helix	52-54	3
β-strand	57-59	3	12
α-helix	61-65	5
α-helix	66-69	4
α-helix	75-83	9
α-helix	86-92	7
α-helix	93-99	7
α-helix	111-130	20
β-strand	136-139	4	12
β-strand	148	1	13
β-strand	151	1	13
β-strand	153	1	14
β-strand	156	1	14
α-helix	160-168	9
β-strand	175-179	5	12
α-helix	186-191	6
β-strand	198-205	8	12
α-helix	222-224	3
β-strand	228-233	6	12
β-strand	238	1	15
α-helix	239-257	19
β-strand	261-265	5	12
α-helix	268-270	3
β-strand	271	1	16
β-strand	280	1	15
β-strand	281	1	16
α-helix	283-294	12
β-strand	300-303	4	12
α-helix	310-325	16
β-strand	332	1	17
α-helix	333-335	3
α-helix	339-342	4
β-strand	347	1	17
α-helix	361-376	16

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 2	A, B, C	protein	369	Homo sapiens	Q92769 (AlphaFold model)

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

>4LY1_1 Histone deacetylase 2 (chains A, B, C)
GKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTK
YHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNR
QQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEA
FYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIIS
KVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIR
NVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRL
FENLRMLPH

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	3
CA	Calcium ion	Ca	3
20Y	4-(acetylamino)-N-[2-amino-5-(thiophen-2-yl)phenyl]benzamide	C19 H17 N3 O2 S	3
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	1

Water and common crystallization additives (NA, PG4) are not listed.

Primary citation

Histone Deacetylase (HDAC) Inhibitor Kinetic Rate Constants Correlate with Cellular Histone Acetylation but Not Transcription and Cell Viability. Lauffer, B.E., Mintzer, R., Fong, R. et al. J Biol Chem (2013) 288:26926-26943. DOI 10.1074/jbc.M113.490706 · 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)
6XDM 1.56 Å, Structure of human HDAC2 in complex with an aryl ketone inhibitor
7ZZT 1.56 Å, Ligand binding to HDAC2
7LTK 1.59 Å, Structure of human HDAC2 in complex with an inhibitor that lacks a zinc binding group…

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