6WSJ | pdb_00006wsj

Crystal Structure of Danio rerio histone deacetylase 6 catalytic domain 2 complexed with cyclopeptide des4.3.1

• PDB DOI: https://doi.org/10.2210/pdb6WSJ/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Danio rerio, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2020-05-01 Released: 2021-04-28 
• Deposition Author(s): Watson, P.R., Christianson, D.W.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.176 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.154 (Depositor), 0.156 (DCC) 
• R-Value Observed: 
  0.155 (Depositor) 

Starting Model: experimental

Literature

Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.

Hosseinzadeh, P., Watson, P.R., Craven, T.W., Li, X., Rettie, S., Pardo-Avila, F., Bera, A.K., Mulligan, V.K., Lu, P., Ford, A.S., Weitzner, B.D., Stewart, L.J., Moyer, A.P., Di Piazza, M., Whalen, J.G., Greisen, P.J., Christianson, D.W., Baker, D.

(2021) Nat Commun 12: 3384-3384

• PubMed: 34099674 
• DOI: https://doi.org/10.1038/s41467-021-23609-8
• Primary Citation Related Structures: 
  6WHN, 6WHO, 6WHQ, 6WHZ, 6WI3, 6WSJ


• PubMed Abstract: 
  

  Despite recent success in computational design of structured cyclic peptides, de novo design of cyclic peptides that bind to any protein functional site remains difficult. To address this challenge, we develop a computational "anchor extension" methodology for targeting protein interfaces by extending a peptide chain around a non-canonical amino acid residue anchor. To test our approach using a well characterized model system, we design cyclic peptides that inhibit histone deacetylases 2 and 6 (HDAC2 and HDAC6) with enhanced potency compared to the original anchor (IC ₅₀ values of 9.1 and 4.4 nM for the best binders compared to 5.4 and 0.6 µM for the anchor, respectively). The HDAC6 inhibitor is among the most potent reported so far. These results highlight the potential for de novo design of high-affinity protein-peptide interfaces, as well as the challenges that remain.

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Organizational Affiliation: 
• University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA.
Knight Campus Center, University of Oregon, Eugene, OR, USA.
Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
Molecular and Cellular Biology Ph.D. Program, University of Washington, Seattle, WA, USA.
Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
Systems Biology, Center for Computational Biology, Flatiron Institute, New York, NY, USA.
Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang Province, China.
Lyell Immunopharma, Inc., Seattle, WA, USA.
Molecular Engineering Ph.D. Program, University of Washington, Seattle, WA, USA.
Novo Nordisk A/S, Måløv, Denmark.
University of Washington, Department of Biochemistry, Institute for Protein Design, Seattle, WA, USA. [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 41.55 kDa 
• Atom Count: 3,062 
• Modeled Residue Count: 361 
• Deposited Residue Count: 372 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hdac6 protein	A	364	Danio rerio	Mutation(s): 0  Gene Names: hdac6
UniProt
Find proteins for F8W4B7 (Danio rerio) Explore F8W4B7  Go to UniProtKB:  F8W4B7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cyclopeptide des4.3.1	B [auth I]	8	synthetic construct	Mutation(s): 0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth A], G [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
K	D [auth A], E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Modified Residues  5 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
DAL	B [auth I]	D-PEPTIDE LINKING	C3 H7 N O2		--
DAR	B [auth I]	D-PEPTIDE LINKING	C6 H15 N4 O2		--
DNE	B [auth I]	D-PEPTIDE LINKING	C6 H13 N O2		--
DSN	B [auth I]	D-PEPTIDE LINKING	C3 H7 N O3		--
U2M	B [auth I]	L-PEPTIDE LINKING	C7 H15 N O2 S		--

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002383	B [auth I]	des4.3.1	Cyclic peptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.176 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.154 (Depositor), 0.156 (DCC) 
• R-Value Observed: 0.155 (Depositor) 

Space Group: P 2 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.5	α = 90
b = 84	β = 90
c = 94.42	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
iMOSFLM	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-04-28 
Deposition Author(s): Watson, P.R., Christianson, D.W.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM49758

Revision History  

• Version 1.0: 2021-04-28
  Type: Initial release
  
• Version 1.1: 2021-09-01
  Changes: Database references
• Version 1.2: 2023-10-18
  Changes: Data collection, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection