2C5O: Cell division protein kinase 2

Differential Binding Of Inhibitors To Active And Inactive Cdk2 Provides Insights For Drug Design. Determined by X-ray diffraction at 2.1 Å resolution. Released 1 Mar 2006.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 9,709
Mol. weight: 128.1 kDa
Ligands: CK2
Released: 1 Mar 2006

Explore 2C5O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2C5O contains 70 α-helices and 26 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: 14 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	1
β-strand	18-23	6	1
β-strand	29-36	8	1
α-helix	46-55	10
β-strand	63	1	2
β-strand	66-71	6	1
β-strand	75-81	7	1
β-strand	85-86	2	2
α-helix	87-93	7
α-helix	101-120	20
β-strand	123-124	2	3
α-helix	130-132	3
β-strand	133-135	3	2
β-strand	141-143	3	2
β-strand	150-151	2	3
β-strand	157	1	4
α-helix	171-174	4
β-strand	179	1	4
α-helix	183-198	16
α-helix	208-219	12
α-helix	230-232	3
α-helix	243-247	5
α-helix	248-251	4
α-helix	257-266	10
α-helix	275-276	2
α-helix	277-282	6
α-helix	284-286	3

Chain B: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	179-192	14
α-helix	194-196	3
α-helix	199-202	4
α-helix	208-224	17
α-helix	229-245	17
α-helix	253-268	16
α-helix	272-274	3
α-helix	275-280	6
α-helix	288-301	14
α-helix	311-318	8
α-helix	319-321	3
α-helix	327-342	16
α-helix	344-347	4
α-helix	352-368	17
α-helix	374-380	7
α-helix	388-400	13
α-helix	401-403	3
α-helix	408-412	5
α-helix	416-418	3
α-helix	425-427	3

Chain C: 16 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	5
β-strand	18-23	6	5
β-strand	29-36	8	5
α-helix	46-57	12
β-strand	63	1	6
β-strand	66-71	6	5
β-strand	75-81	7	5
β-strand	85-86	2	6
α-helix	87-93	7
α-helix	101-120	20
β-strand	123-124	2	7
α-helix	130-132	3
β-strand	133-135	3	6
β-strand	141-143	3	6
β-strand	150-151	2	7
α-helix	155-156	2
β-strand	157	1	8
α-helix	158	1
α-helix	171-174	4
β-strand	179	1	8
α-helix	183-198	16
α-helix	208-219	12
α-helix	230-232	3
α-helix	243-247	5
α-helix	248-251	4
α-helix	257-266	10
α-helix	275-276	2
α-helix	277-282	6
α-helix	284-288	5

Chain D: 20 helices, 0 β-strands

Element	Residues	Length
α-helix	179-192	14
α-helix	194-196	3
α-helix	199-201	3
α-helix	208-224	17
α-helix	229-243	15
α-helix	253-268	16
α-helix	272-274	3
α-helix	275-280	6
α-helix	288-301	14
α-helix	311-318	8
α-helix	319-321	3
α-helix	327-342	16
α-helix	344-347	4
α-helix	352-368	17
α-helix	374-380	7
α-helix	388-400	13
α-helix	401-403	3
α-helix	408-413	6
α-helix	416-418	3
α-helix	425-427	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cell division protein kinase 2	A, C	protein	298	HOMO SAPIENS	P24941 (AlphaFold model)
Cyclin A2	B, D	protein	260	HOMO SAPIENS	P20248 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>2C5O_1 CELL DIVISION PROTEIN KINASE 2 (chains A, C)
MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNH
PNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHS
HRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYY
STAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSF
PKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL

Sequence of entity 2 (B, D), FASTA

>2C5O_2 CYCLIN A2 (chains B, D)
NEVPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETL
HLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVL
RMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLP
SVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREK
YKNSKYHGVSLLNPPETLNL

Ligands and cofactors

ID	Name	Formula	Copies
CK2	4-(2,4-dimethyl-1,3-thiazol-5-yl)pyrimidin-2-amine	C9 H10 N4 S	2

Primary citation

Differential Binding of Inhibitors to Active and Inactive Cdk2 Provides Insights for Drug Design. Kontopidis, G., Mcinnes, C., Pandalaneni, S.R. et al. Chem Biol (2006) 13:201. DOI 10.1016/J.CHEMBIOL.2005.11.011 · PubMed

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

6Q4G 0.98 Å, CDK2 in complex with FragLite37
6Q49 1.0 Å, CDK2 in complex with FragLite6
6Q4H 1.0 Å, CDK2 in complex with FragLite36
6Q48 1.03 Å, CDK2 in complex with FragLite7
6Q4J 1.05 Å, CDK2 in complex with FragLite34
6Q4E 1.06 Å, CDK2 in complex with FragLite33
6Q4K 1.06 Å, CDK2 in complex with FragLite38
6Q4D 1.07 Å, CDK2 in complex with FragLite31
6Q3B 1.11 Å, CDK2 in complex with FragLite2
6Q4I 1.11 Å, CDK2 in complex with FragLite35
6Q4B 1.12 Å, CDK2 in complex with FragLite13
6Q4A 1.13 Å, CDK2 in complex with FragLite14

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