8G3E: Human WDR5

Crystal structure of human WDR5 in complex with (1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-yl)-1,4-dihydropyridazine-3-carboxamide (compound 2, WDR5-MYC inhibitor). Determined by X-ray diffraction at 1.33 Å resolution. Released 28 Jun 2023.

Method: X-ray diffraction
Resolution: 1.33 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,480
Mol. weight: 70.19 kDa
Ligands: YJR
Released: 28 Jun 2023

Explore 8G3E in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8G3E contains 1 α-helix and 58 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, 29 β-strands

Element	Residues	Length	Sheet
β-strand	36-41	6	1
β-strand	48-53	6	2
β-strand	59-64	6	2
β-strand	69-73	5	2
β-strand	79-83	5	2
β-strand	90-95	6	3
β-strand	101-106	6	3
β-strand	110-115	6	3
β-strand	120-126	7	3
β-strand	132-137	6	4
β-strand	143-148	6	4
β-strand	153-157	5	4
β-strand	163-167	5	4
β-strand	174-179	6	5
β-strand	185-190	6	5
β-strand	195-199	5	5
β-strand	205-209	5	5
β-strand	217-222	6	6
β-strand	229-233	5	6
β-strand	237-242	6	6
β-strand	247-252	6	6
β-strand	264-267	4	7
β-strand	273-276	4	7
β-strand	278	1	1
β-strand	283-287	5	7
β-strand	293-297	5	7
β-strand	304-309	6	1
β-strand	315-320	6	1
β-strand	327-331	5	1

Chain B: 1 helix, 29 β-strands

Element	Residues	Length	Sheet
β-strand	36-41	6	8
β-strand	48-53	6	9
β-strand	59-64	6	9
β-strand	68-73	6	9
β-strand	79-84	6	9
β-strand	90-95	6	10
β-strand	101-106	6	10
β-strand	110-115	6	10
β-strand	121-126	6	10
β-strand	132-137	6	11
β-strand	143-148	6	11
β-strand	153-157	5	11
β-strand	163-167	5	11
β-strand	174-179	6	12
β-strand	185-190	6	12
β-strand	195-199	5	12
β-strand	205-209	5	12
α-helix	215-216	2
β-strand	217-222	6	13
β-strand	228-233	6	13
β-strand	237-242	6	13
β-strand	247-252	6	13
β-strand	264-267	4	14
β-strand	273-276	4	14
β-strand	278	1	8
β-strand	283-287	5	14
β-strand	293-297	5	14
β-strand	304-309	6	8
β-strand	315-320	6	8
β-strand	327-331	5	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
WD repeat-containing protein 5	A, B	protein	316	Homo sapiens	P61964 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8G3E_1 WD repeat-containing protein 5 (chains A, B)
SNASATQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGK
FEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFN
PQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIW
DTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNE
KYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIAS
AALENDKTIKLWKSDC

Ligands and cofactors

ID	Name	Formula	Copies
YJR	(1M)-N-[(3,5-difluoro[1,1'-biphenyl]-4-yl)methyl]-6-methyl-4-oxo-1-(pyridin-3-y…	C24 H18 F2 N4 O2	2

Primary citation

Discovery and Structure-Based Design of Inhibitors of the WD Repeat-Containing Protein 5 (WDR5)-MYC Interaction. Ding, J., Liu, L., Chiang, Y.L. et al. J Med Chem (2023) 66:8310-8323. DOI 10.1021/acs.jmedchem.3c00787 · 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
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
7WVK 1.42 Å, Crystal structure of human WDR5 in complex with compound 19

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