5VD2: Human WEE1 kinase domain

crystal structure of human WEE1 kinase domain in complex with PF-03814735. Determined by X-ray diffraction at 2.05 Å resolution. Released 23 Aug 2017.

Method: X-ray diffraction
Resolution: 2.05 Å
Organism: Homo sapiens
Chains: 1
Atoms: 2,146
Mol. weight: 33.08 kDa
Ligands: 34W, PO4
Released: 23 Aug 2017

Explore 5VD2 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VD2 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	333-334	2
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	432-435	4	2
β-strand	458-461	4	2
β-strand	468-469	2	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	530-533	4
α-helix	540-549	10
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

>5VD2_1 Wee1-like protein kinase (chains A)
GAGSMKSRYTTEFHELEKIGSGEFGSVFKCVKRLDGCIYAIKRSKKPLAGSVDEQNALRE
VYAHAVLGQHSHVVRYFSAWAEDDHMLIQNEYCNGGSLADAISENYRIMSYFKEAELKDL
LLQVGRGLRYIHSMSLVHMDIKPSNIFISRTSIPNAASEEGDEDDWASNKVMFKIGDLGH
VTRISSPQVEEGDSRFLANEVLQENYTHLPKADIFALALTVVCAAGAEPLPRNGDQWHEI
RQGRLPRIPQVLSQEFTELLKVMIHPDPERRPSAMALVKHSVLLSASRK

Ligands and cofactors

ID	Name	Formula	Copies
34W	N-{2-[(1S,4R)-6-{[4-(cyclobutylamino)-5-(trifluoromethyl)pyrimidin-2-yl]amino}-…	C23 H25 F3 N6 O2	1
PO4	Phosphate ion	O4 P	1

Water and common crystallization additives (CL) 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
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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