9YV4: Human DCAF1 WDR domain

Crystal structure of the human DCAF1 WDR domain in complex with OICR-41109. Determined by X-ray diffraction at 1.6 Å resolution. Released 26 Nov 2025.

Method: X-ray diffraction
Resolution: 1.6 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,469
Mol. weight: 72.32 kDa
Ligands: A1CY9
Released: 26 Nov 2025

Explore 9YV4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9YV4 contains 6 α-helices and 62 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: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	1081-1086	6	1
β-strand	1095	1	1
β-strand	1096-1101	6	2
β-strand	1107-1112	6	2
β-strand	1116-1121	6	2
β-strand	1127-1132	6	2
β-strand	1138-1143	6	3
β-strand	1149-1154	6	3
β-strand	1161-1166	6	3
β-strand	1170-1176	7	3
β-strand	1181-1184	4	4
β-strand	1191-1196	6	4
β-strand	1199-1204	6	4
β-strand	1210-1214	5	4
β-strand	1229-1230	2	5
β-strand	1236-1239	4	5
β-strand	1242-1245	4	5
β-strand	1250-1254	5	5
α-helix	1255-1257	3
β-strand	1264-1266	3	6
β-strand	1272-1275	4	6
β-strand	1278-1281	4	6
β-strand	1287-1290	4	6
α-helix	1292-1294	3
β-strand	1297-1301	5	7
β-strand	1307-1312	6	7
β-strand	1313	1	8
α-helix	1314-1315	2
β-strand	1330	1	8
β-strand	1333-1338	6	7
β-strand	1344-1349	6	7
β-strand	1354-1359	6	1
β-strand	1365-1371	7	1
β-strand	1382-1388	7	1

Chain B: 3 helices, 31 β-strands

Element	Residues	Length	Sheet
β-strand	1080-1086	7	9
β-strand	1095	1	9
β-strand	1096-1101	6	10
β-strand	1107-1112	6	10
β-strand	1116-1121	6	10
β-strand	1127-1132	6	10
β-strand	1138-1143	6	11
β-strand	1149-1154	6	11
β-strand	1161-1166	6	11
β-strand	1170-1176	7	11
β-strand	1181-1184	4	12
β-strand	1191-1196	6	12
β-strand	1199-1204	6	12
β-strand	1210-1214	5	12
β-strand	1229-1230	2	13
β-strand	1236-1239	4	13
β-strand	1242-1245	4	13
β-strand	1250-1254	5	13
α-helix	1255-1257	3
β-strand	1264-1266	3	14
β-strand	1272-1275	4	14
β-strand	1278-1281	4	14
β-strand	1287-1290	4	14
α-helix	1292-1294	3
β-strand	1297-1301	5	15
β-strand	1307-1312	6	15
β-strand	1313	1	16
α-helix	1314-1315	2
β-strand	1330	1	16
β-strand	1333-1338	6	15
β-strand	1344-1349	6	15
β-strand	1354-1359	6	9
β-strand	1365-1371	7	9
β-strand	1382-1389	8	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
DDB1- and CUL4-associated factor 1	A, B	protein	315	Homo sapiens	Q9Y4B6 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9YV4_1 DDB1- and CUL4-associated factor 1 (chains A, B)
GASAFRPISVFREANEDESGFTCCAFSARERFLMLGTCTGQLKLYNVFSGQEEASYNCHN
SAITHLEPSRDGSLLLTSATWSQPLSALWGMKSVFDMKHSFTEDHYVEFSKHSQDRVIGT
KGDIAHIYDIQTGNKLLTLFNPDLANNYKRNCATFNPTDDLVLNDGVLWDVRSAQAIHKF
DKFNMNISGVFHPNGLEVIINTEIWDLRTFHLLHTVPALDQCRVVFNHTGTVMYGAMLQA
DDEDDLMEERMKSPFGSSFRTFNATDYKPIATIDVKRNIFDLCTDTKDCYLAVIENQGSM
DALNMDTVCRLYEVG

Ligands and cofactors

ID	Name	Formula	Copies
A1CY9	(4P)-4-(4-chloro-2-fluorophenyl)-N-[(1S)-1-(3-chloro-4-fluorophenyl)-2-cyanoeth…	C27 H22 Cl2 F2 N4 O2	2

Water and common crystallization additives (NA, UNX) are not listed.

Primary citation

OICR-41103 as a chemical probe for the DCAF1 WD40 domain. Kimani, S.W., Noureldin, M., Wilson, B. et al. Commun Biol (2025) 8:1076-1076. DOI 10.1038/s42003-025-08491-0 · PubMed

Other PDB entries of the same protein (UniProt Q9Y4B6 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9PLY 1.4 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-40156
9BHS 1.43 Å, Crystal structure of the WDR domain of human DCAF1 in complex with OICR-9939 compound
9Y4Q 1.48 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-40102
8OOD 1.5 Å, Crystal structure of human DCAF1 WD40 repeats (Q1250L) in complex with compound 15
9YDG 1.54 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-41074
8F8E 1.55 Å, Crystal structure of the WDR domain of human DCAF1 in complex with OICR-8268 compound
9Y76 1.56 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-40120
7SSE 1.62 Å, Crystal structure of the WDR domain of human DCAF1 in complex with CYCA-117-70
9BHR 1.62 Å, Crystal structure of the WDR domain of human DCAF1 in complex with OICR-40155 compound
9D4E 1.7 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-41103
4PXW 1.72 Å, Crystal structure of human DCAF1 WD40 repeats (Q1250L)
9YE4 1.74 Å, Crystal structure of the human DCAF1 WDR domain in complex with OICR-41110

Browse structure collections

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