7QHL: Cyclin-dependent kinase 2/cyclin A

Crystal structure of Cyclin-dependent kinase 2/cyclin A in complex with 3,5,7-Substituted pyrazolo[4,3-d]pyrimidine inhibitor 24. Determined by X-ray diffraction at 1.7 Å resolution. Released 6 Jul 2022.

Method
X-ray diffraction
Resolution
1.7 Å
Organism
Homo sapiens
Chains
4
Atoms
9,960
Mol. weight
129.58 kDa
Ligands
D5P, SGM
Released
6 Jul 2022

Explore 7QHL in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

7QHL contains 72 α-helices and 22 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-strand18-2361
β-strand29-3571
α-helix46-5611
β-strand6312
α-helix64-652
β-strand66-7051
β-strand76-8161
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
Chains B and D: 20 helices, 0 β-strands
ElementResiduesLengthSheet
α-helix179-19214
α-helix194-1963
α-helix199-2024
α-helix208-22417
α-helix229-24315
α-helix250-26819
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: 16 helices, 11 β-strands
ElementResiduesLengthSheet
β-strand4-1184
β-strand18-2364
β-strand29-3684
α-helix46-5611
β-strand6315
α-helix64-652
β-strand66-7164
β-strand75-8174
β-strand85-8625
α-helix87-937
α-helix101-12020
β-strand123-12426
α-helix130-1323
β-strand133-13535
β-strand141-14335
β-strand150-15126
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

Molecules and chains

MoleculeChainsTypeLengthOrganismUniProt
Cyclin-dependent kinase 2A, Cprotein299Homo sapiensP24941 (AlphaFold model)
Cyclin-A2B, Dprotein258Homo sapiensP20248 (AlphaFold model)
Sequence of entity 1 (A, C), FASTA
>7QHL_1 Cyclin-dependent kinase 2 (chains A, C)
SMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELN
HPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCH
SHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKY
YSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPS
FPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL
Sequence of entity 2 (B, D), FASTA
>7QHL_2 Cyclin-A2 (chains B, D)
VPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHL
AVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRM
EHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSV
IAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYK
NSKYHGVSLLNPPETLNL

Ligands and cofactors

IDNameFormulaCopies
D5P5-(2-amino-1-ethyl)thio-3-cyclobutyl-7-[4-(pyrazol-1-yl)benzyl]amino-1(2)H-pyra…C21 H24 N8 S2
SGMMonothioglycerolC3 H8 O2 S3

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

Primary citation

3,5,7-Substituted Pyrazolo[4,3- d ]Pyrimidine Inhibitors of Cyclin-Dependent Kinases and Cyclin K Degraders. Jorda, R., Havlicek, L., Perina, M. et al. J Med Chem (2022) 65:8881-8896. DOI 10.1021/acs.jmedchem.1c02184 · PubMed

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

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