6U6K | pdb_00006u6k

BRD4-BD1 in complex with the cyclic peptide 3.1_3

• PDB DOI: https://doi.org/10.2210/pdb6U6K/pdb

• Classification: Transcription/Inhibitor
• Organism(s): Homo sapiens, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-08-30 Released: 2020-08-19 
• Deposition Author(s): Patel, K., Walshe, J.L., Walport, L.J., Mackay, J.P.
• Funding Organization(s): National Health and Medical Research Council (NHMRC, Australia)

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Cyclic peptides can engage a single binding pocket through highly divergent modes.

Patel, K., Walport, L.J., Walshe, J.L., Solomon, P.D., Low, J.K.K., Tran, D.H., Mouradian, K.S., Silva, A.P.G., Wilkinson-White, L., Norman, A., Franck, C., Matthews, J.M., Guss, J.M., Payne, R.J., Passioura, T., Suga, H., Mackay, J.P.

(2020) Proc Natl Acad Sci U S A 117: 26728-26738

• PubMed: 33046654 
• DOI: https://doi.org/10.1073/pnas.2003086117
• Primary Citation Related Structures: 
  6U4A, 6U61, 6U6K, 6U6L, 6U71, 6U72, 6U74, 6U8G, 6U8H, 6U8I, 6U8M, 6ULP, 6ULQ, 6ULT, 6ULV


• PubMed Abstract: 
  

  Cyclic peptide library screening technologies show immense promise for identifying drug leads and chemical probes for challenging targets. However, the structural and functional diversity encoded within such libraries is largely undefined. We have systematically profiled the affinity, selectivity, and structural features of library-derived cyclic peptides selected to recognize three closely related targets: the acetyllysine-binding bromodomain proteins BRD2, -3, and -4. We report affinities as low as 100 pM and specificities of up to 10 ⁶ -fold. Crystal structures of 13 peptide-bromodomain complexes reveal remarkable diversity in both structure and binding mode, including both α-helical and β-sheet structures as well as bivalent binding modes. The peptides can also exhibit a high degree of structural preorganization. Our data demonstrate the enormous potential within these libraries to provide diverse binding modes against a single target, which underpins their capacity to yield highly potent and selective ligands.

---

Organizational Affiliation: 
• School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia.
Protein-Protein Interaction Laboratory, The Francis Crick Institute, London NW1 1AT, United Kingdom; [e-mail] [e-mail] [e-mail].
Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London W12 0BZ, United Kingdom.
Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.
School of Chemistry, The University of Sydney, Sydney, NSW 2006, Australia.
Sydney Analytical Core Research Facility, The University of Sydney, NSW 2006, Australia.
Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan; [e-mail] [e-mail] [e-mail].
School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW 2006, Australia; [e-mail] [e-mail] [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

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

Biological Assembly Evidence: surface plasmon resonance

Macromolecule Content 

• Total Structure Weight: 18.67 kDa 
• Atom Count: 1,266 
• Modeled Residue Count: 139 
• Deposited Residue Count: 159 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Bromodomain-containing protein 4	A	146	Homo sapiens	Mutation(s): 0  Gene Names: BRD4, HUNK1
UniProt & NIH Common Fund Data Resources
Find proteins for O60885 (Homo sapiens) Explore O60885  Go to UniProtKB:  O60885
PHAROS:  O60885 GTEx:  ENSG00000141867

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
cyclic peptide 3.1_3	B [auth C]	13	synthetic construct	Mutation(s): 0

Small Molecules

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B [auth C]	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.218 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 121.957	α = 90
b = 41.903	β = 94.204
c = 29.538	γ = 90

Software Package:

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

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2020-08-19 
Deposition Author(s): Patel, K., Walshe, J.L., Walport, L.J., Mackay, J.P.

---

Funding Organization	Location	Grant Number
National Health and Medical Research Council (NHMRC, Australia)	Australia	APP1161623

Revision History  

• Version 1.0: 2020-08-19
  Type: Initial release
  
• Version 1.1: 2021-03-03
  Changes: Database references
• Version 1.2: 2023-10-11
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.3: 2023-11-15
  Changes: Data collection
• Version 1.4: 2024-10-09
  Changes: Structure summary