5V5Y: Human WEE1 kinase domain

Crystal structure of human WEE1 kinase domain in complex with MK1775. Determined by X-ray diffraction at 1.9 Å resolution. Released 23 Aug 2017.

Method: X-ray diffraction
Resolution: 1.9 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,226
Mol. weight: 33.22 kDa
Ligands: 8X7
Released: 23 Aug 2017

Explore 5V5Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5V5Y contains 19 α-helices and 12 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: 19 helices, 12 β-strands

Element	Residues	Length	Sheet
α-helix	294-298	5
β-strand	299-307	9	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	356	1	2
β-strand	359	1	2
α-helix	360-361	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	475-477	3
α-helix	480-482	3
α-helix	485-488	4
α-helix	495-510	16
α-helix	513-517	5
α-helix	521-527	7
α-helix	531-533	3
α-helix	540-548	9
α-helix	554-556	3
α-helix	558-559	2
α-helix	560-564	5

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

>5V5Y_1 Wee1-like protein kinase (chains A)
GAGSMKSRYTTEFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALRE
VYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDL
LLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGH
VTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEI
RQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVLLSASRK

Ligands and cofactors

ID	Name	Formula	Copies
8X7	1-[6-(2-hydroxypropan-2-yl)pyridin-2-yl]-6-{[4-(4-methylpiperazin-1-yl)phenyl]a…	C27 H32 N8 O2	1

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

Primary citation

Structural Basis of Wee Kinases Functionality and Inactivation by Diverse Small Molecule Inhibitors. Zhu, J.Y., Cuellar, R.A., Berndt, N. et al. J Med Chem (2017) 60:7863-7875. DOI 10.1021/acs.jmedchem.7b00996 · 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
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
5VD4 2.02 Å, Crystal structure of human WEE1 kinase domain in complex with rac-IV-016, a MK1775…

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