5VD7: Human WEE1 kinase domain

Crystal structure of human WEE1 kinase domain in complex with rac-IV-098, a MK1775 analogue. Determined by X-ray diffraction at 2.08 Å resolution. Released 4 Apr 2018.

Method: X-ray diffraction
Resolution: 2.08 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,190
Mol. weight: 33.06 kDa
Ligands: 99V
Released: 4 Apr 2018

Explore 5VD7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VD7 contains 16 α-helices and 11 β-strands across 1 chain. 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	384-394	11
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
β-strand	468-469	2	3
α-helix	480-482	3
α-helix	485-488	4
α-helix	496-510	15
α-helix	513-517	5
α-helix	521-527	7
α-helix	531-533	3
α-helix	540-549	10
α-helix	558-559	2
α-helix	560-564	5
α-helix	567-569	3

Molecules and chains

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

Sequence of entity 1 (A), FASTA

>5VD7_1 Wee1-like protein kinase (chains A)
GAGSMKSRYTTEFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALRE
VYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDL
LLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGH
VTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEI
RQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVLLSASRK

Ligands and cofactors

ID	Name	Formula	Copies
99V	6-{[3-fluoro-4-(4-methylpiperazin-1-yl)phenyl]amino}-1-[6-(2-hydroxypropan-2-yl…	C27 H31 F N8 O2	1

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

Primary citation

Structural basis of Wee family kinase inhibition by small molecules. Zhu, J.-Y., Schonbrunn, E. To be published.

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
9D0Q 1.96 Å, Crystal structure of human Wee1 kinase domain in complex with inhibitor
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

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