8Q1N: Cyclic peptide binder of the WBM-site of WDR5

Cyclic peptide binder of the WBM-site of WDR5. Determined by X-ray diffraction at 1.84 Å resolution. Released 6 Sept 2023.

Method: X-ray diffraction
Resolution: 1.84 Å
Organism: Homo sapiens
Chains: 4
Atoms: 5,614
Mol. weight: 73.11 kDa
Released: 6 Sept 2023

Explore 8Q1N in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8Q1N contains 0 α-helices and 60 β-strands across 2 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: 0 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	32-33	2	1
β-strand	36-41	6	2
β-strand	48-53	6	3
β-strand	59-64	6	3
β-strand	68-73	6	3
β-strand	79-84	6	3
β-strand	90-95	6	4
β-strand	101-106	6	4
β-strand	111-115	5	4
β-strand	120-125	6	4
β-strand	132-137	6	5
β-strand	143-148	6	5
β-strand	153-157	5	5
β-strand	163-167	5	5
β-strand	174-179	6	6
β-strand	185-190	6	6
β-strand	195-199	5	6
β-strand	205-209	5	6
β-strand	217-222	6	7
β-strand	228-233	6	7
β-strand	237-242	6	7
β-strand	247-252	6	7
β-strand	264-267	4	8
β-strand	273-276	4	8
β-strand	282-287	6	8
β-strand	293-298	6	8
β-strand	304-309	6	2
β-strand	315-320	6	2
β-strand	327-331	5	2
β-strand	335-336	2	1

Chain B: 0 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	29-32	4	9
β-strand	35-41	7	10
β-strand	48-53	6	11
β-strand	59-64	6	11
β-strand	69-73	5	11
β-strand	79-83	5	11
β-strand	90-95	6	12
β-strand	101-106	6	12
β-strand	111-115	5	12
β-strand	120-125	6	12
β-strand	132-137	6	13
β-strand	143-148	6	13
β-strand	153-157	5	13
β-strand	163-167	5	13
β-strand	174-179	6	14
β-strand	185-190	6	14
β-strand	195-199	5	14
β-strand	205-209	5	14
β-strand	217-222	6	15
β-strand	228-233	6	15
β-strand	237-242	6	15
β-strand	247-252	6	15
β-strand	264-267	4	16
β-strand	273-276	4	16
β-strand	283-287	5	16
β-strand	293-297	5	16
β-strand	304-309	6	10
β-strand	315-320	6	10
β-strand	327-332	6	10
β-strand	336-338	3	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
WD repeat-containing protein 5	A, B	protein	321	Homo sapiens	P61964 (AlphaFold model)
Cyclic peptide inhibitor	a, b	protein	11	Homo sapiens	P01106 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8Q1N_1 WD repeat-containing protein 5 (chains A, B)
SATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEK
TISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQS
NLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTA
SGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYC
IFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAAL
ENDKTIKLWKSDCGTLEVLFQ

Sequence of entity 2 (a, b), FASTA

>8Q1N_2 Cyclic peptide inhibitor (chains a, b)
DEEEIDVVAVE

Primary citation

Macrocyclic peptides as inhibitors of WDR5-lncRNA interactions. Chang, J.Y., Neugebauer, C., Schmeing, S. et al. Chem Commun (Camb) (2023) 59:10656-10659. DOI 10.1039/d3cc03221c · PubMed

Other PDB entries of the same protein (UniProt P61964 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6E1Z 1.1 Å, Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with…
6U6W 1.2 Å, Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the…
6E1Y 1.22 Å, Discovery of Potent 2-Aryl-6,7-Dihydro-5HPyrrolo[ 1,2-a]imidazoles as WDR5 WIN-site…
6UHZ 1.26 Å, WDR5 in complex with Myc site fragment inhibitor
6UHY 1.26 Å, WDR5 in complex with Myc site fragment inhibitor
7BED 1.26 Å, X-ray structure of WDR5 bound to the WDR5 win motif peptide
6U8B 1.26 Å, Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the…
24XP 1.3 Å, Crystal structure of WDR5 F133A variant in complex with MBD3C
4ERY 1.3 Å, X-ray structure of WDR5-MLL3 Win motif peptide binary complex
8G3E 1.33 Å, Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl…
3EMH 1.37 Å, Structural basis of WDR5-MLL interaction
3UVK 1.4 Å, Crystal structure of WDR5 in complex with the WDR5-interacting motif of MLL2

Browse structure collections

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