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Bromine in PDB 9esk: CDK2-Cyclin A in Complex with Fraglite 30

Enzymatic activity of CDK2-Cyclin A in Complex with Fraglite 30

All present enzymatic activity of CDK2-Cyclin A in Complex with Fraglite 30:
2.7.11.22;

Protein crystallography data

The structure of CDK2-Cyclin A in Complex with Fraglite 30, PDB code: 9esk was solved by I.Hope, M.P.Martin, M.J.Waring, M.E.M.Noble, J.A.Endicott, N.J.Tatum, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 73.98 / 2.40
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.092, 134.078, 147.75, 90, 90, 90
R / Rfree (%) 21.1 / 21.7

Bromine Binding Sites:

The binding sites of Bromine atom in the CDK2-Cyclin A in Complex with Fraglite 30 (pdb code 9esk). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 9 binding sites of Bromine where determined in the CDK2-Cyclin A in Complex with Fraglite 30, PDB code: 9esk:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9;

Bromine binding site 1 out of 9 in 9esk

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Bromine binding site 1 out of 9 in the CDK2-Cyclin A in Complex with Fraglite 30


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of CDK2-Cyclin A in Complex with Fraglite 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br601

b:73.5
occ:1.00
 BR A:W3D601 0.0 73.5 1.0
C5 A:W3D601 1.9 73.4 1.0
C6 A:W3D601 2.8 70.3 1.0
C4 A:W3D601 2.9 61.7 1.0
O A:LEU83 3.2 52.8 1.0
N A:LEU83 3.6 47.5 1.0
CD1 A:PHE82 3.8 49.7 1.0
CB A:ALA31 4.0 36.6 1.0
CD1 A:LEU134 4.1 44.8 1.0
C3 A:W3D601 4.1 63.1 1.0
CD1 A:ILE10 4.2 48.0 1.0
C A:W3D601 4.2 67.8 1.0
C A:LEU83 4.2 51.8 1.0
CE1 A:PHE82 4.3 49.3 1.0
CA A:PHE82 4.3 48.4 1.0
CA A:LEU83 4.4 48.3 1.0
C A:PHE82 4.5 44.8 1.0
O A:GLU81 4.5 50.1 1.0
CG A:PHE82 4.6 48.6 1.0
N A:W3D601 4.6 67.5 1.0
CB A:LEU83 4.7 41.0 1.0
CB A:PHE82 4.9 51.5 1.0
CD2 A:LEU134 4.9 48.4 1.0

Bromine binding site 2 out of 9 in 9esk

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Bromine binding site 2 out of 9 in the CDK2-Cyclin A in Complex with Fraglite 30


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of CDK2-Cyclin A in Complex with Fraglite 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br602

b:163.2
occ:0.50
 BR A:W3D602 0.0 163.2 0.5
BR A:W3D602 1.6 164.5 0.5
C5 A:W3D602 1.9 153.6 0.5
C5 A:W3D602 2.2 126.1 0.5
C6 A:W3D602 2.4 106.9 0.5
CB A:LYS6 2.8 73.3 1.0
C6 A:W3D602 2.8 140.1 0.5
C4 A:W3D602 2.9 145.8 0.5
C4 A:W3D602 3.5 118.0 0.5
CA A:LYS6 3.5 66.3 1.0
C A:W3D602 3.8 100.6 0.5
CD1 A:LEU32 3.9 47.1 1.0
N A:LYS6 4.0 65.2 1.0
CG A:TYR19 4.1 70.8 1.0
CB A:TYR19 4.1 58.0 1.0
C3 A:W3D602 4.1 129.0 0.5
C A:W3D602 4.2 123.3 0.5
CD2 A:TYR19 4.4 75.1 1.0
CD1 A:TYR19 4.4 78.2 1.0
O A:W3D602 4.5 103.9 0.5
C3 A:W3D602 4.5 106.6 0.5
N A:W3D602 4.6 102.0 0.5
N A:W3D602 4.7 117.7 0.5
CB A:ALA21 4.7 53.2 1.0
C A:LYS6 4.9 65.2 1.0
C A:GLN5 5.0 64.2 1.0
CE2 A:TYR19 5.0 93.7 1.0

Bromine binding site 3 out of 9 in 9esk

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Bromine binding site 3 out of 9 in the CDK2-Cyclin A in Complex with Fraglite 30


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of CDK2-Cyclin A in Complex with Fraglite 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br602

b:164.5
occ:0.50
 BR A:W3D602 0.0 164.5 0.5
C5 A:W3D602 1.3 153.6 0.5
BR A:W3D602 1.6 163.2 0.5
C5 A:W3D602 1.9 126.1 0.5
C6 A:W3D602 2.1 140.1 0.5
C4 A:W3D602 2.2 145.8 0.5
C6 A:W3D602 2.8 106.9 0.5
C4 A:W3D602 2.9 118.0 0.5
C3 A:W3D602 3.3 129.0 0.5
C A:W3D602 3.3 123.3 0.5
CD1 A:TYR19 3.5 78.2 1.0
N A:W3D602 3.7 117.7 0.5
CG A:TYR19 3.7 70.8 1.0
CE1 A:TYR19 4.0 94.1 1.0
CB A:LYS6 4.0 73.3 1.0
CB A:TYR19 4.1 58.0 1.0
C3 A:W3D602 4.1 106.6 0.5
CD1 A:LEU32 4.2 47.1 1.0
C A:W3D602 4.2 100.6 0.5
CD2 A:TYR19 4.2 75.1 1.0
O A:W3D602 4.3 113.8 0.5
CZ A:TYR19 4.5 113.8 1.0
CE1 A:TYR77 4.6 71.6 1.0
CE2 A:TYR19 4.6 93.7 1.0
N A:W3D602 4.6 102.0 0.5
CB A:LEU32 4.8 47.0 1.0
OH A:TYR77 5.0 101.1 1.0

Bromine binding site 4 out of 9 in 9esk

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Bromine binding site 4 out of 9 in the CDK2-Cyclin A in Complex with Fraglite 30


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of CDK2-Cyclin A in Complex with Fraglite 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br603

b:137.5
occ:1.00
 BR A:W3D603 0.0 137.5 1.0
C5 A:W3D603 1.9 178.8 1.0
C6 A:W3D603 2.8 201.4 1.0
C4 A:W3D603 2.8 151.4 1.0
CG A:PRO253 3.8 46.1 1.0
C3 A:W3D603 4.1 148.7 1.0
C A:W3D603 4.2 202.1 1.0
CB A:PRO253 4.3 46.9 1.0
CA A:LYS250 4.4 55.8 1.0
CG A:LYS250 4.5 57.9 1.0
O A:SER249 4.6 54.1 1.0
N A:W3D603 4.6 178.6 1.0
CB A:LYS250 4.7 56.0 1.0
O A:LYS250 4.9 69.9 1.0

Bromine binding site 5 out of 9 in 9esk

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Bromine binding site 5 out of 9 in the CDK2-Cyclin A in Complex with Fraglite 30


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of CDK2-Cyclin A in Complex with Fraglite 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br501

b:122.3
occ:1.00
 BR B:W3D501 0.0 122.3 1.0
C5 B:W3D501 1.9 142.8 1.0
C6 B:W3D501 2.8 154.1 1.0
C4 B:W3D501 2.8 142.4 1.0
BR B:W3D502 3.4 121.2 1.0
OE1 B:GLN254 3.7 59.5 1.0
CG B:TRP217 3.7 46.0 1.0
CD B:GLN254 3.8 59.2 1.0
CD2 B:TRP217 3.8 41.8 1.0
CB B:TRP217 3.8 45.2 1.0
CE3 B:TRP217 4.0 39.9 1.0
CG B:GLN254 4.0 56.4 1.0
C3 B:W3D501 4.1 154.8 1.0
C B:W3D501 4.2 176.5 1.0
CD1 B:TRP217 4.3 46.8 1.0
NE2 B:GLN254 4.4 61.8 1.0
C5 B:W3D502 4.4 152.3 1.0
CE2 B:TRP217 4.4 48.8 1.0
C4 B:W3D502 4.5 150.7 1.0
CD1 B:LEU214 4.6 49.6 1.0
CB B:GLN254 4.6 60.5 1.0
CA B:LEU214 4.6 51.6 1.0
N B:W3D501 4.6 177.1 1.0
NE1 B:TRP217 4.7 46.7 1.0
O B:ILE213 4.7 52.0 1.0
CG2 B:ILE213 4.7 50.1 1.0
CZ3 B:TRP217 4.8 46.5 1.0

Bromine binding site 6 out of 9 in 9esk

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Bromine binding site 6 out of 9 in the CDK2-Cyclin A in Complex with Fraglite 30


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of CDK2-Cyclin A in Complex with Fraglite 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br502

b:121.2
occ:1.00
 BR B:W3D502 0.0 121.2 1.0
C5 B:W3D502 1.9 152.3 1.0
C4 B:W3D502 2.8 150.7 1.0
C6 B:W3D502 2.9 122.2 1.0
BR B:W3D501 3.4 122.3 1.0
C6 B:W3D501 3.5 154.1 1.0
C5 B:W3D501 3.6 142.8 1.0
CB B:LEU214 3.9 48.8 1.0
CD1 B:LEU214 3.9 49.6 1.0
CB B:GLN254 4.1 60.5 1.0
C3 B:W3D502 4.1 140.9 1.0
N B:GLN254 4.1 53.7 1.0
O B:HOH638 4.2 58.5 1.0
C B:W3D502 4.2 115.7 1.0
CA B:LEU214 4.2 51.6 1.0
CA B:GLN254 4.3 61.2 1.0
CD2 B:LEU253 4.4 43.9 1.0
N B:LEU214 4.5 47.8 1.0
CG B:LEU253 4.5 43.5 1.0
CG B:LEU214 4.5 49.4 1.0
O B:MET210 4.5 57.1 1.0
C B:W3D501 4.5 176.5 1.0
C4 B:W3D501 4.6 142.4 1.0
N B:W3D502 4.6 137.1 1.0
CG B:GLN254 4.7 56.4 1.0
CB B:LEU253 4.7 46.2 1.0
CG2 B:ILE213 4.8 50.1 1.0
C B:LEU253 4.8 54.2 1.0

Bromine binding site 7 out of 9 in 9esk

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Bromine binding site 7 out of 9 in the CDK2-Cyclin A in Complex with Fraglite 30


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of CDK2-Cyclin A in Complex with Fraglite 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br501

b:69.7
occ:1.00
 BR C:W3D501 0.0 69.7 1.0
C5 C:W3D501 1.9 67.8 1.0
C6 C:W3D501 2.8 61.9 1.0
C4 C:W3D501 2.8 53.5 1.0
O C:LEU83 3.3 54.8 1.0
N C:LEU83 3.4 50.1 1.0
C3 C:W3D501 4.1 56.9 1.0
C C:LEU83 4.1 58.4 1.0
C C:W3D501 4.2 67.4 1.0
CD1 C:LEU134 4.2 52.1 1.0
CB C:ALA31 4.2 36.9 1.0
CD1 C:PHE82 4.2 57.8 1.0
CA C:LEU83 4.2 56.7 1.0
CA C:PHE82 4.2 48.2 1.0
C C:PHE82 4.3 49.2 1.0
O C:GLU81 4.4 56.4 1.0
CD2 C:LEU134 4.5 49.5 1.0
CB C:LEU83 4.5 56.4 1.0
CD1 C:ILE10 4.5 72.0 1.0
CE1 C:PHE82 4.6 59.9 1.0
N C:W3D501 4.6 63.3 1.0
CG C:PHE82 4.8 55.9 1.0
CG C:LEU134 4.9 54.0 1.0

Bromine binding site 8 out of 9 in 9esk

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Bromine binding site 8 out of 9 in the CDK2-Cyclin A in Complex with Fraglite 30


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of CDK2-Cyclin A in Complex with Fraglite 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br502

b:149.4
occ:1.00
 BR C:W3D502 0.0 149.4 1.0
C5 C:W3D502 1.9 136.2 1.0
C6 C:W3D502 2.8 116.6 1.0
C4 C:W3D502 2.9 141.9 1.0
CD1 C:TYR19 3.5 93.3 1.0
CE C:LYS6 3.7 104.6 1.0
CG C:TYR19 3.9 84.5 1.0
CE1 C:TYR19 3.9 104.4 1.0
CD1 C:LEU32 3.9 54.2 1.0
C3 C:W3D502 4.1 141.7 1.0
C C:W3D502 4.1 131.6 1.0
CE1 C:TYR77 4.3 73.2 1.0
CB C:TYR19 4.3 68.4 1.0
NZ C:LYS6 4.4 89.6 1.0
CD2 C:TYR19 4.5 89.5 1.0
CZ C:TYR19 4.5 103.5 1.0
CB C:LEU32 4.6 47.5 1.0
N C:W3D502 4.6 142.1 1.0
CB C:LYS6 4.7 72.8 1.0
CE2 C:TYR19 4.8 93.5 1.0
CD C:LYS6 4.8 100.5 1.0
CD1 C:TYR77 4.8 59.9 1.0
CG C:LEU32 4.9 50.6 1.0
CG C:LYS6 5.0 91.9 1.0

Bromine binding site 9 out of 9 in 9esk

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Bromine binding site 9 out of 9 in the CDK2-Cyclin A in Complex with Fraglite 30


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 9 of CDK2-Cyclin A in Complex with Fraglite 30 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br501

b:139.4
occ:1.00
 BR D:W3D501 0.0 139.4 1.0
C5 D:W3D501 1.9 156.8 1.0
C4 D:W3D501 2.8 156.8 1.0
C6 D:W3D501 2.9 161.4 1.0
OE1 D:GLN254 3.8 61.6 1.0
CD D:GLN254 3.8 59.8 1.0
CG D:GLN254 4.1 49.8 1.0
C3 D:W3D501 4.1 173.0 1.0
CB D:TRP217 4.1 53.9 1.0
CG D:TRP217 4.2 57.4 1.0
CD2 D:TRP217 4.2 54.2 1.0
C D:W3D501 4.2 171.4 1.0
NE2 D:GLN254 4.2 59.0 1.0
CE3 D:TRP217 4.2 51.6 1.0
CG2 D:ILE213 4.3 53.2 1.0
CA D:LEU214 4.4 45.5 1.0
CB D:GLN254 4.5 48.8 1.0
CD1 D:LEU214 4.5 43.4 1.0
N D:W3D501 4.6 176.8 1.0
O D:ILE213 4.7 50.4 1.0
N D:LEU214 4.7 47.6 1.0
CD1 D:TRP217 4.9 57.7 1.0
C D:ILE213 4.9 49.2 1.0
CE2 D:TRP217 4.9 56.5 1.0
CZ3 D:TRP217 5.0 53.3 1.0

Reference:

I.Hope, M.P.Martin, M.J.Waring, M.E.M.Noble, J.A.Endicott, N.J.Tatum. Crystallographic Fragment Screening of CDK2-Cyclin A: Fraglites Map Sites of Protein-Protein Interaction To Be Published.
Page generated: Mon Jul 7 12:47:25 2025

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