9B9W: WD repeat-containing protein 5

Crystal structure of the ternary complex of DCAF1 and WDR5 with PROTAC, OICR-40792. Determined by X-ray diffraction at 1.92 Å resolution. Released 6 Nov 2024.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,354
Mol. weight: 76.08 kDa
Ligands: A1ANN
Released: 6 Nov 2024

Explore 9B9W in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9B9W 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: 0 helices, 28 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	68-73	6	2
β-strand	79-84	6	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	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: 3 helices, 28 β-strands

Element	Residues	Length	Sheet
β-strand	1081-1087	7	8
β-strand	1096-1101	6	9
β-strand	1107-1112	6	9
β-strand	1116-1121	6	9
β-strand	1127-1132	6	9
β-strand	1138-1143	6	10
β-strand	1149-1154	6	10
β-strand	1161-1165	5	10
β-strand	1171-1176	6	10
β-strand	1181-1184	4	11
β-strand	1191-1196	6	11
β-strand	1199-1204	6	11
β-strand	1210-1214	5	11
β-strand	1229-1230	2	12
β-strand	1236-1239	4	12
β-strand	1242-1245	4	12
β-strand	1250-1254	5	12
α-helix	1255-1257	3
β-strand	1265-1266	2	13
β-strand	1272-1275	4	13
β-strand	1278-1281	4	13
β-strand	1287-1290	4	13
α-helix	1292-1294	3
β-strand	1297-1301	5	14
β-strand	1307-1313	7	14
α-helix	1314	1
β-strand	1330-1338	9	14
β-strand	1344-1349	6	14
β-strand	1353-1359	7	8
β-strand	1365-1371	7	8
β-strand	1382-1388	7	8

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
WD repeat-containing protein 5	A	protein	329	Homo sapiens	P61964 (AlphaFold model)
DDB1- and CUL4-associated factor 1	B	protein	338	Homo sapiens	Q9Y4B6 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>9B9W_1 WD repeat-containing protein 5 (chains A)
MHHHHHHSSGRENLYFQGTQSKPTPVKPNYALKFTLAGHTKAVSSVKFSPNGEWLASSSA
DKLIKIWGAYDGKFEKTISGHKLGISDVAWSSDSNLLVSASDDKTLKIWDVSSGKCLKTL
KGHSNYVFCCNFNPQSNLIVSGSFDESVRIWDVKTGKCLKTLPAHSDPVSAVHFNRDGSL
IVSSSYDGLCRIWDTASGQCLKTLIDDDNPPVSFVKFSPNGKYILAATLDNTLKLWDYSK
GKCLKTYTGHKNEKYCIFANFSVTGGKWIVSGSEDNLVYIWNLQTKEIVQKLQGHTDVVI
STACHPTENIIASAALENDKTIKLWKSDC

Sequence of entity 2 (B), FASTA

>9B9W_2 DDB1- and CUL4-associated factor 1 (chains B)
MGSSHHHHHHSSGRENLYFQGSSRASAFRPISVFREANEDESGFTCCAFSARERFLMLGT
CTGQLKLYNVFSGQEEASYNCHNSAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDM
KHSFTEDHYVEFSKHSQDRVIGTKGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNP
TDDLVLNDGVLWDVRSAQAIHKFDKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVP
ALDQCRVVFNHTGTVMYGAMLQADDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKR
NIFDLCTDTKDCYLAVIENQGSMDALNMDTVCRLYEVG

Ligands and cofactors

ID	Name	Formula	Copies
A1ANN	(4P)-N-[(1R)-3-amino-1-(3-chloro-4-fluorophenyl)-3-oxopropyl]-4-(4-chloro-2-flu…	C65 H71 Cl2 F7 N8 O11	1

Primary citation

Crystal structures of DCAF1-PROTAC-WDR5 ternary complexes provide insight into DCAF1 substrate specificity. Mabanglo, M.F., Wilson, B., Noureldin, M. et al. Nat Commun (2024) 15:10165-10165. DOI 10.1038/s41467-024-54500-x · 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

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