6U8B: WD repeat-containing protein 5

Discovery and optimization of salicyclic acid-derived sulfonamide inhibitors of the WDR5:MYC protein-protein interaction. Determined by X-ray diffraction at 1.26 Å resolution. Released 4 Dec 2019.

Method: X-ray diffraction
Resolution: 1.26 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,895
Mol. weight: 69.34 kDa
Ligands: Q1M
Released: 4 Dec 2019

Explore 6U8B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U8B contains 3 α-helices and 56 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: 2 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	27-30	4
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	111-115	5	3
β-strand	121-125	5	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
α-helix	215-216	2
β-strand	217-222	6	6
β-strand	228-233	6	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	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, 28 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	69-73	5	9
β-strand	79-83	5	9
β-strand	90-95	6	10
β-strand	101-106	6	10
β-strand	110-115	6	10
β-strand	120-126	7	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	194-199	6	12
β-strand	205-210	6	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	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	311	Homo sapiens	P61964 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6U8B_1 WD repeat-containing protein 5 (chains A, B)
TQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSADKLIKIWGAYDGKFEKTI
SGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTLKGHSNYVFCCNFNPQSNL
IVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSLIVSSSYDGLCRIWDTASG
QCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSKGKCLKTYTGHKNEKYCIF
ANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVISTACHPTENIIASAALEN
DKTIKLWKSDC

Ligands and cofactors

ID	Name	Formula	Copies
Q1M	3-{[(5-bromo-2-methoxyphenyl)sulfonyl]amino}-5-chloro-2-hydroxybenzoic acid	C14 H11 Br Cl N O6 S	2

Primary citation

Discovery and Optimization of Salicylic Acid-Derived Sulfonamide Inhibitors of the WD Repeat-Containing Protein 5-MYC Protein-Protein Interaction. Macdonald, J.D., Chacon Simon, S., Han, C. et al. J Med Chem (2019) 62:11232-11259. DOI 10.1021/acs.jmedchem.9b01411 · PubMed

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

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