5CYI: Cyclin-dependent kinase 2

CDK2/Cyclin A covalent complex with 6-(cyclohexylmethoxy)-N-(4-(vinylsulfonyl)phenyl)-9H-purin-2-amine (NU6300). Determined by X-ray diffraction at 2.0 Å resolution. Released 16 Sept 2015.

Method
X-ray diffraction
Resolution
2.0 Å
Organism
Homo sapiens
Chains
4
Atoms
9,513
Mol. weight
129.54 kDa
Ligands
55S
Released
16 Sept 2015

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

Secondary structure: helices and β-sheets

5CYI contains 75 α-helices and 24 β-strands across 4 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

ElementResiduesLengthSheet
β-strand4-1181
β-strand17-2371
β-strand29-3681
α-helix46-5712
β-strand6312
β-strand66-7161
β-strand75-8171
β-strand85-8622
α-helix87-937
α-helix101-12020
β-strand123-12423
α-helix130-1323
β-strand133-13532
β-strand141-14332
β-strand150-15123
α-helix166-1683
α-helix171-1744
α-helix183-19816
α-helix208-21912
α-helix230-2323
α-helix243-2475
α-helix248-2514
α-helix257-26610
α-helix275-2762
α-helix277-2815
α-helix284-2863
α-helix292-2943
Chain B: 21 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix176-1783
α-helix179-19214
α-helix199-2024
α-helix208-22417
α-helix229-24517
α-helix250-2523
α-helix253-26816
α-helix272-2743
α-helix275-2817
α-helix288-30114
α-helix311-3199
α-helix327-34216
α-helix344-3474
α-helix352-36817
α-helix374-3807
α-helix384-40017
α-helix401-4033
α-helix408-4125
α-helix416-4183
α-helix421-4233
α-helix425-4273
Chain C: 17 helices, 13 β-strands
ElementResiduesLengthSheet
β-strand4-1184
β-strand17-2374
β-strand29-3684
β-strand3815
β-strand4315
α-helix46-5712
β-strand6316
β-strand66-7164
β-strand75-8174
β-strand85-8626
α-helix87-937
α-helix101-12020
β-strand123-12427
α-helix130-1323
β-strand133-13536
β-strand141-14336
α-helix146-1483
β-strand150-15127
α-helix166-1683
α-helix171-1744
α-helix183-19816
α-helix208-21912
α-helix230-2323
α-helix243-2475
α-helix248-2514
α-helix257-26610
α-helix275-2762
α-helix277-2815
α-helix284-2863
α-helix292-2943
Chain D: 21 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix179-19214
α-helix194-1963
α-helix199-2024
α-helix208-22417
α-helix229-24517
α-helix250-2523
α-helix253-26816
α-helix272-2743
α-helix275-2817
α-helix288-30114
α-helix311-3199
α-helix327-34216
α-helix344-3474
α-helix352-36817
α-helix374-3807
α-helix384-40017
α-helix401-4033
α-helix408-4125
α-helix416-4183
α-helix421-4233
α-helix425-4273

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cyclin-dependent kinase 2A, Cprotein303Homo sapiensP24941 (AlphaFold model)
Cyclin-A2B, Dprotein260Homo sapiensP20248 (AlphaFold model)
Sequence of entity 1 (A, C), FASTA
>5CYI_1 Cyclin-dependent kinase 2 (chains A, C)
GPLGSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLL
KELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGL
AFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILL
GCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPD
YKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPH
LRL
Sequence of entity 2 (B, D), FASTA
>5CYI_2 Cyclin-A2 (chains B, D)
MEVPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETL
HLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVL
RMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLP
SVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREK
YKNSKYHGVSLLNPPETLNL

Ligands and cofactors

IDNameFormulaCopies
55S6-(cyclohexylmethoxy)-N-[4-(ethylsulfonyl)phenyl]-9H-purin-2-amineC20 H25 N5 O3 S2

Primary citation

Identification and Characterization of an Irreversible Inhibitor of CDK2. Anscombe, E., Meschini, E., Mora-Vidal, R. et al. Chem Biol (2015) 22:1159-1164. DOI 10.1016/j.chembiol.2015.07.018 · PubMed

Other PDB entries of the same protein (UniProt P24941 (AlphaFold model), which also has an AlphaFold model), best resolution first:

Browse structure collections

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