4CFV: Cyclin-dependent kinase 2

Structure-based design of C8-substituted O6-cyclohexylmethoxyguanine CDK1 and 2 inhibitors. Determined by X-ray diffraction at 2.0 Å resolution. Released 10 Dec 2014.

Method: X-ray diffraction
Resolution: 2.0 Å
Organism: HOMO SAPIENS
Chains: 4
Atoms: 9,640
Mol. weight: 129.77 kDa
Ligands: MG, 75X
Released: 10 Dec 2014

Explore 4CFV in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4CFV contains 76 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: 19 helices, 11 β-strands

Element	Residues	Length	Sheet
α-helix	1-3	3
β-strand	4-13	10	1
β-strand	16-23	8	1
β-strand	29-36	8	1
α-helix	46-57	12
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
α-helix	146-148	3
β-strand	150-151	2	3
α-helix	156-158	3
α-helix	166-168	3
α-helix	171-174	4
α-helix	183-198	16
α-helix	208-219	12
α-helix	230-232	3
α-helix	243-246	4
α-helix	248-251	4
α-helix	257-266	10
α-helix	275-276	2
α-helix	277-280	4
α-helix	284-288	5
α-helix	292-294	3

Chains B and D: 21 helices, 0 β-strands

Element	Residues	Length
α-helix	172-174	3
α-helix	179-192	14
α-helix	194-196	3
α-helix	199-202	4
α-helix	208-224	17
α-helix	229-243	15
α-helix	250-268	19
α-helix	272-274	3
α-helix	275-281	7
α-helix	288-301	14
α-helix	311-319	9
α-helix	327-342	16
α-helix	344-347	4
α-helix	352-368	17
α-helix	374-380	7
α-helix	384-400	17
α-helix	401-403	3
α-helix	408-412	5
α-helix	416-418	3
α-helix	421-423	3
α-helix	425-427	3

Chain C: 15 helices, 13 β-strands

Element	Residues	Length	Sheet
β-strand	4-11	8	4
β-strand	17-23	7	4
β-strand	29-36	8	4
β-strand	38	1	5
β-strand	43	1	5
α-helix	46-57	12
β-strand	63	1	6
α-helix	64-65	2
β-strand	66-71	6	4
β-strand	75-81	7	4
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
α-helix	146-148	3
β-strand	150-151	2	7
α-helix	166-168	3
α-helix	171-174	4
α-helix	183-198	16
α-helix	208-219	12
α-helix	257-266	10
α-helix	275-276	2
α-helix	277-281	5
α-helix	284-288	5
α-helix	292-294	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Cyclin-dependent kinase 2	A, C	protein	303	HOMO SAPIENS	P24941 (AlphaFold model)
Cyclin-A2	B, D	protein	262	HOMO SAPIENS	P20248 (AlphaFold model)

Sequence of entity 1 (A, C), FASTA

>4CFV_1 CYCLIN-DEPENDENT KINASE 2 (chains A, C)
GPPGSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLL
KELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGL
AFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILL
GCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPD
YKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPH
LRL

Sequence of entity 2 (B, D), FASTA

>4CFV_2 CYCLIN-A2 (chains B, D)
GVNEVPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNE
TLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQ
VLRMEHLVLKVLTFDLAAPTINQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKY
LPSVIAAAAFHLALYTVTGQSWPESLVQKTGYTLETLKPCLLDLHQTYLRAPQHAQQSIR
EKYKNSKYHGVSLLNPPETLNL

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	4
75X	3-[2-amino-6-(cyclohexylmethoxy)-7H-purin-8-yl]-2-methylphenol	C19 H23 N5 O2	2

Primary citation

8-Substituted O6-Cyclohexylmethylguanine Cdk2 Inhibitors; Using Structure-Based Inhibitor Design to Optimise an Alternative Binding Mode. Carbain, B., Paterson, D.J., Anscombe, E. et al. J Med Chem (2014) 57:56. DOI 10.1021/JM401555V · 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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