6WHN: Histone deacetylase 2

Histone deacetylases complex with peptide macrocycles. Determined by X-ray diffraction at 1.54 Å resolution. Released 21 Apr 2021.

Method: X-ray diffraction
Resolution: 1.54 Å
Organisms: Homo sapiens, synthetic construct
Chains: 6
Atoms: 10,346
Mol. weight: 137.32 kDa
Ligands: NHE, ZN
Released: 21 Apr 2021

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

Secondary structure: helices and β-sheets

6WHN contains 59 α-helices and 50 β-strands across 5 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	160-169	10
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	283-294	12
β-strand	300-303	4	1
α-helix	310-325	16
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, 16 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	86-92	7
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
α-helix	239-257	19
β-strand	261-265	5	6
α-helix	268-270	3
β-strand	271	1	9
β-strand	281	1	9
α-helix	283-294	12
β-strand	300-303	4	6
α-helix	310-324	15
β-strand	332	1	10
α-helix	333-335	3
α-helix	339-342	4
β-strand	347	1	10
α-helix	361-375	15

Chain C: 19 helices, 18 β-strands

Element	Residues	Length	Sheet
β-strand	16-19	4	11
α-helix	24-26	3
α-helix	38-49	12
α-helix	52-55	4
β-strand	57-59	3	11
α-helix	60-65	6
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	11
β-strand	148	1	12
β-strand	151	1	12
β-strand	153	1	13
β-strand	156	1	13
α-helix	160-168	9
β-strand	175-179	5	11
α-helix	186-191	6
β-strand	198-205	8	11
α-helix	222-224	3
β-strand	228-233	6	11
β-strand	238	1	14
α-helix	239-257	19
β-strand	261-265	5	11
α-helix	268-270	3
β-strand	271	1	15
β-strand	280	1	14
β-strand	281	1	15
α-helix	283-294	12
β-strand	300-303	4	11
α-helix	310-324	15
β-strand	332	1	16
α-helix	333-335	3
α-helix	339-342	4
β-strand	347	1	16
α-helix	361-375	15

Chains G and H: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	502-504	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Histone deacetylase 2	A, B, C	protein	385	Homo sapiens	Q92769 (AlphaFold model)
U2M-ASN-PRO-LYS-GLN-DLY-TRP-GLY peptide macrocycle	F, G, H	protein	8	synthetic construct

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

>6WHN_1 Histone deacetylase 2 (chains A, B, C)
AAYSQGGGKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKA
TAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVA
GAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHH
GDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQ
IFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLG
GGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYM
EKIKQRLFENLRMLPHAPGVQMQAI

Sequence of entity 2 (F, G, H), FASTA

>6WHN_2 U2M-ASN-PRO-LYS-GLN-DLY-TRP-GLY peptide macrocycle (chains F, G, H)
XNPKQKWG

Ligands and cofactors

ID	Name	Formula	Copies
NHE	2-[N-cyclohexylamino]ethane sulfonic acid	C8 H17 N O3 S	2
ZN	Zinc ion	Zn	3

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

Primary citation

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites. Hosseinzadeh, P., Watson, P.R., Craven, T.W. et al. Nat Commun (2021) 12:3384-3384. DOI 10.1038/s41467-021-23609-8 · 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
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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