9D0Q: Human Wee1 kinase domain

Crystal structure of human Wee1 kinase domain in complex with inhibitor. Determined by X-ray diffraction at 1.96 Å resolution. Released 10 Sept 2025.

Method: X-ray diffraction
Resolution: 1.96 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,756
Mol. weight: 66.67 kDa
Ligands: A1A1S
Released: 10 Sept 2025

Explore 9D0Q in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9D0Q contains 33 α-helices and 22 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: 16 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	294-298	5
β-strand	299-308	10	1
β-strand	311-318	8	1
β-strand	324-331	8	1
α-helix	332-334	3
α-helix	338-353	16
β-strand	359	1	2
β-strand	362-368	7	1
β-strand	371-377	7	1
β-strand	383	1	2
α-helix	384-393	10
α-helix	400-419	20
β-strand	422-423	2	3
α-helix	429-431	3
β-strand	432-436	5	2
β-strand	457-461	5	2
α-helix	464-466	3
β-strand	468-469	2	3
α-helix	485-488	4
α-helix	495-510	16
α-helix	521-527	7
α-helix	530-533	4
α-helix	540-549	10
α-helix	554-556	3
α-helix	558-559	2
α-helix	560-564	5
α-helix	567-570	4

Chain B: 17 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	294-298	5
β-strand	299-307	9	4
β-strand	311-318	8	4
β-strand	324-331	8	4
α-helix	332-334	3
α-helix	338-353	16
β-strand	359	1	5
β-strand	362-368	7	4
β-strand	371-377	7	4
β-strand	383	1	5
α-helix	384-394	11
α-helix	400-419	20
β-strand	422-423	2	6
α-helix	429-431	3
β-strand	432-437	6	5
β-strand	456-461	6	5
α-helix	464-466	3
β-strand	468-469	2	6
α-helix	480-482	3
α-helix	485-488	4
α-helix	495-510	16
α-helix	521-527	7
α-helix	530-533	4
α-helix	540-549	10
α-helix	554-556	3
α-helix	558-559	2
α-helix	560-564	5
α-helix	567-572	6

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Wee1-like protein kinase	A, B	protein	289	Homo sapiens	P30291 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9D0Q_1 Wee1-like protein kinase (chains A, B)
GAMGMKSRYTTEFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALRE
VYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDL
LLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGH
VTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEI
RQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVLLSASRK

Ligands and cofactors

ID	Name	Formula	Copies
A1A1S	1-[(6R)-6-(2,6-dichlorophenyl)-8-methyl-2-[4-(4-methylpiperazin-1-yl)anilino]-7…	C26 H29 Cl2 N7 O	2

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

Primary citation

Harnessing free energy calculations for kinome-wide selectivity in drug discovery campaigns with a Wee1 case study. Knight, J.L., Clark, A.J., Wang, J. et al. Nat Commun (2025) 16:7962-7962. DOI 10.1038/s41467-025-62722-w · PubMed

Other PDB entries of the same protein (UniProt P30291 (AlphaFold model), which also has an AlphaFold model), best resolution first:

8BJU 1.53 Å, HUMAN WEE1 KINASE IN COMPLEX WITH INHIBITOR 1-[6-(1-Hydroxy-1-methyl-ethyl)-pyridin-2-yl]…
9D0S 1.64 Å, Crystal structure of human Wee1 kinase domain in complex with inhibitor
9TG7 1.68 Å, Crystal structure of beta-TrCP bound by monophosphorylated WEE1 degron peptide
1X8B 1.81 Å, Structure of human Wee1A kinase: kinase domain complexed with inhibitor PD0407824
5VD8 1.85 Å, Crystal structure of human WEE1 kinase domain in complex with RAC-IV-099, a MK1775…
5VD9 1.87 Å, Crystal structure of human WEE1 kinase domain in complex with RAC-IV-097, a MK1775…
2IN6 1.9 Å, Wee1 kinase complex with inhibitor PD311839
5V5Y 1.9 Å, Crystal structure of human WEE1 kinase domain in complex with MK1775
5VC5 1.93 Å, Crystal structure of human WEE1 kinase domain in complex with PD-166285
5VC3 1.97 Å, Crystal structure of human WEE1 kinase domain in complex with bosutinib
5VC6 2.0 Å, crystal structure of human WEE1 kinase domain in complex with PHA-848125
5VD4 2.02 Å, Crystal structure of human WEE1 kinase domain in complex with rac-IV-016, a MK1775…

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