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Iodine in PDB 9etb: CDK2-Cyclin A in Complex with Fraglite 2

Enzymatic activity of CDK2-Cyclin A in Complex with Fraglite 2

All present enzymatic activity of CDK2-Cyclin A in Complex with Fraglite 2:
2.7.11.22;

Protein crystallography data

The structure of CDK2-Cyclin A in Complex with Fraglite 2, PDB code: 9etb 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) 99.38 / 2.76
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.151, 133.667, 147.94, 90, 90, 90
R / Rfree (%) 21.2 / 22.8

Iodine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 16;

Binding sites:

The binding sites of Iodine atom in the CDK2-Cyclin A in Complex with Fraglite 2 (pdb code 9etb). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 16 binding sites of Iodine where determined in the CDK2-Cyclin A in Complex with Fraglite 2, PDB code: 9etb:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Iodine binding site 1 out of 16 in 9etb

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Iodine binding site 1 out of 16 in the CDK2-Cyclin A in Complex with Fraglite 2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 1 of CDK2-Cyclin A in Complex with Fraglite 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:I501

b:73.1
occ:1.00
I4 D:PYZ501 0.0 73.1 1.0
C4 D:PYZ501 2.1 67.8 1.0
C3 D:PYZ501 3.0 67.5 1.0
C5 D:PYZ501 3.1 69.9 1.0
CD D:GLN254 3.7 38.8 1.0
CG D:GLN254 3.9 35.5 1.0
CD1 D:LEU214 4.0 24.8 1.0
NE2 D:GLN254 4.0 40.7 1.0
OE1 D:GLN254 4.1 42.1 1.0
CB D:GLN254 4.1 35.3 1.0
N2 D:PYZ501 4.1 81.0 1.0
CB D:TRP217 4.1 36.4 1.0
CE3 D:TRP217 4.1 30.1 1.0
CD2 D:TRP217 4.1 32.1 1.0
CG D:TRP217 4.2 35.2 1.0
N1 D:PYZ501 4.2 86.6 1.0
CA D:LEU214 4.3 29.3 1.0
CG2 D:ILE213 4.4 32.8 1.0
O D:ILE213 4.6 31.4 1.0
CA D:GLN254 4.7 33.8 1.0
N D:LEU214 4.7 29.9 1.0
CB D:LEU214 4.9 26.9 1.0
C D:ILE213 4.9 31.3 1.0
CZ3 D:TRP217 4.9 29.6 1.0
CD1 D:TRP217 4.9 36.0 1.0
CE2 D:TRP217 4.9 33.6 1.0
O D:HOH624 5.0 33.5 1.0

Iodine binding site 2 out of 16 in 9etb

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Iodine binding site 2 out of 16 in the CDK2-Cyclin A in Complex with Fraglite 2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 2 of CDK2-Cyclin A in Complex with Fraglite 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I601

b:68.0
occ:1.00
I4 A:PYZ601 0.0 68.0 1.0
C4 A:PYZ601 2.1 56.5 1.0
C3 A:PYZ601 3.1 55.9 1.0
C5 A:PYZ601 3.1 60.6 1.0
O A:HOH709 3.8 41.3 1.0
CG1 A:VAL289 4.1 35.1 1.0
O A:PHE286 4.2 35.8 1.0
CZ A:PHE109 4.2 29.7 1.0
N2 A:PYZ601 4.3 56.1 1.0
N1 A:PYZ601 4.3 59.1 1.0
CE2 A:PHE109 4.6 29.9 1.0
CE1 A:PHE109 4.9 28.1 1.0

Iodine binding site 3 out of 16 in 9etb

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Iodine binding site 3 out of 16 in the CDK2-Cyclin A in Complex with Fraglite 2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 3 of CDK2-Cyclin A in Complex with Fraglite 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I602

b:34.5
occ:0.50
I4 A:PYZ602 0.0 34.5 0.5
C3 A:PYZ602 1.8 35.0 0.5
C4 A:PYZ602 2.1 35.5 0.5
N2 A:PYZ602 2.8 34.5 0.5
C4 A:PYZ602 2.9 35.4 0.5
C3 A:PYZ602 3.1 36.6 0.5
C5 A:PYZ602 3.1 34.7 0.5
I4 A:PYZ602 3.7 35.7 0.5
N1 A:PYZ602 4.0 34.7 0.5
C5 A:PYZ602 4.0 35.7 0.5
CG A:PHE80 4.0 28.4 1.0
CD1 A:PHE80 4.1 29.7 1.0
CB A:PHE80 4.2 27.9 1.0
N2 A:PYZ602 4.2 36.5 0.5
N1 A:PYZ602 4.3 35.5 0.5
CD1 A:LEU134 4.3 31.1 1.0
CE A:LYS33 4.3 64.8 1.0
CD2 A:PHE80 4.4 27.8 1.0
CB A:ALA31 4.5 29.1 1.0
CE1 A:PHE80 4.5 30.5 1.0
CG1 A:VAL18 4.6 39.0 1.0
CG2 A:VAL64 4.7 27.8 1.0
CE2 A:PHE80 4.8 26.9 1.0
CZ A:PHE80 4.9 28.0 1.0
NZ A:LYS33 4.9 61.8 1.0

Iodine binding site 4 out of 16 in 9etb

Go back to Iodine Binding Sites List in 9etb
Iodine binding site 4 out of 16 in the CDK2-Cyclin A in Complex with Fraglite 2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 4 of CDK2-Cyclin A in Complex with Fraglite 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I602

b:35.7
occ:0.50
I4 A:PYZ602 0.0 35.7 0.5
C4 A:PYZ602 2.1 35.4 0.5
C3 A:PYZ602 2.1 36.6 0.5
C4 A:PYZ602 3.0 35.5 0.5
C3 A:PYZ602 3.1 35.0 0.5
C5 A:PYZ602 3.1 35.7 0.5
N2 A:PYZ602 3.2 36.5 0.5
I4 A:PYZ602 3.7 34.5 0.5
CG2 A:VAL18 3.9 41.3 1.0
CG1 A:VAL18 3.9 39.0 1.0
CB A:VAL18 4.0 39.5 1.0
N2 A:PYZ602 4.2 34.5 0.5
C5 A:PYZ602 4.2 34.7 0.5
N1 A:PYZ602 4.2 34.7 0.5
N1 A:PYZ602 4.3 35.5 0.5
CD1 A:LEU134 4.7 31.1 1.0
CD1 A:ILE10 4.7 53.6 1.0
CG1 A:ILE10 4.9 54.6 1.0

Iodine binding site 5 out of 16 in 9etb

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Iodine binding site 5 out of 16 in the CDK2-Cyclin A in Complex with Fraglite 2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 5 of CDK2-Cyclin A in Complex with Fraglite 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I604

b:72.1
occ:0.50
I4 A:PYZ604 0.0 72.1 0.5
I4 A:PYZ604 0.3 99.1 0.5
C4 A:PYZ604 2.0 74.0 0.5
C4 A:PYZ604 2.1 55.2 0.5
C3 A:PYZ604 3.0 66.2 0.5
C5 A:PYZ604 3.0 73.3 0.5
C3 A:PYZ604 3.1 51.6 0.5
C5 A:PYZ604 3.1 53.5 0.5
CD A:LYS6 3.5 64.6 1.0
CG A:LYS6 3.5 59.3 1.0
O A:HOH744 3.9 34.3 1.0
CD1 A:LEU32 4.0 39.8 1.0
N2 A:PYZ604 4.1 66.1 0.5
N1 A:PYZ604 4.1 70.3 0.5
CB A:TYR19 4.2 53.5 1.0
N2 A:PYZ604 4.2 51.5 0.5
N1 A:PYZ604 4.2 53.0 0.5
CE A:LYS6 4.2 64.7 1.0
CE1 A:TYR77 4.3 47.5 1.0
CG A:TYR19 4.4 63.1 1.0
CB A:LEU32 4.4 38.4 1.0
CD1 A:TYR19 4.7 73.5 1.0
CD2 A:TYR19 4.8 67.8 1.0
CG A:LEU32 4.8 38.3 1.0
CD1 A:TYR77 4.9 44.8 1.0

Iodine binding site 6 out of 16 in 9etb

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Iodine binding site 6 out of 16 in the CDK2-Cyclin A in Complex with Fraglite 2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 6 of CDK2-Cyclin A in Complex with Fraglite 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I604

b:99.1
occ:0.50
I4 A:PYZ604 0.0 99.1 0.5
I4 A:PYZ604 0.3 72.1 0.5
C4 A:PYZ604 1.9 55.2 0.5
C4 A:PYZ604 2.1 74.0 0.5
C5 A:PYZ604 2.9 53.5 0.5
C3 A:PYZ604 3.0 51.6 0.5
C3 A:PYZ604 3.1 66.2 0.5
C5 A:PYZ604 3.1 73.3 0.5
CD A:LYS6 3.6 64.6 1.0
CG A:LYS6 3.7 59.3 1.0
O A:HOH744 3.8 34.3 1.0
CD1 A:LEU32 3.9 39.8 1.0
N1 A:PYZ604 4.0 53.0 0.5
N2 A:PYZ604 4.0 51.5 0.5
CE1 A:TYR77 4.1 47.5 1.0
N2 A:PYZ604 4.2 66.1 0.5
N1 A:PYZ604 4.2 70.3 0.5
CE A:LYS6 4.4 64.7 1.0
CB A:LEU32 4.4 38.4 1.0
CB A:TYR19 4.5 53.5 1.0
CG A:TYR19 4.6 63.1 1.0
CD1 A:TYR77 4.7 44.8 1.0
CG A:LEU32 4.8 38.3 1.0
CZ A:TYR77 5.0 50.8 1.0
CE A:MET1 5.0 51.6 1.0

Iodine binding site 7 out of 16 in 9etb

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Iodine binding site 7 out of 16 in the CDK2-Cyclin A in Complex with Fraglite 2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 7 of CDK2-Cyclin A in Complex with Fraglite 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I606

b:89.5
occ:1.00
I4 A:PYZ606 0.0 89.5 1.0
C4 A:PYZ606 2.1 75.2 1.0
C3 A:PYZ606 3.1 78.0 1.0
C5 A:PYZ606 3.1 70.6 1.0
CB A:PRO254 3.9 40.3 1.0
O A:PRO254 4.0 43.4 1.0
C A:PRO254 4.2 41.9 1.0
N2 A:PYZ606 4.2 78.9 1.0
N1 A:PYZ606 4.2 76.9 1.0
CG1 A:VAL197 4.3 34.0 1.0
CD1 A:LEU101 4.5 30.9 1.0
N A:LEU255 4.6 40.1 1.0
CA A:PRO254 4.6 41.3 1.0
CD1 A:LEU255 4.8 37.0 1.0
CA A:LEU255 4.8 41.2 1.0

Iodine binding site 8 out of 16 in 9etb

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Iodine binding site 8 out of 16 in the CDK2-Cyclin A in Complex with Fraglite 2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 8 of CDK2-Cyclin A in Complex with Fraglite 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I501

b:91.3
occ:1.00
I4 B:PYZ501 0.0 91.3 1.0
C4 B:PYZ501 2.1 102.5 1.0
C3 B:PYZ501 3.1 99.1 1.0
C5 B:PYZ501 3.1 96.0 1.0
I4 B:PYZ502 3.6 103.6 1.0
CG B:TRP217 3.9 34.7 1.0
CB B:TRP217 4.0 33.9 1.0
CD2 B:TRP217 4.0 36.0 1.0
OE1 B:GLN254 4.0 37.9 1.0
CD B:GLN254 4.0 38.5 1.0
CE3 B:TRP217 4.2 34.6 1.0
CG B:GLN254 4.2 36.0 1.0
N2 B:PYZ501 4.2 93.9 1.0
N1 B:PYZ501 4.3 94.2 1.0
CD1 B:TRP217 4.5 35.9 1.0
CA B:LEU214 4.6 32.6 1.0
CE2 B:TRP217 4.6 37.2 1.0
NE2 B:GLN254 4.6 40.2 1.0
CG2 B:ILE213 4.7 39.5 1.0
CD1 B:LEU214 4.8 30.9 1.0
CB B:GLN254 4.8 36.4 1.0
NE1 B:TRP217 4.9 37.1 1.0
CZ3 B:TRP217 4.9 35.5 1.0
O B:ILE213 4.9 40.2 1.0
C4 B:PYZ502 4.9 77.7 1.0

Iodine binding site 9 out of 16 in 9etb

Go back to Iodine Binding Sites List in 9etb
Iodine binding site 9 out of 16 in the CDK2-Cyclin A in Complex with Fraglite 2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 9 of CDK2-Cyclin A in Complex with Fraglite 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I502

b:103.6
occ:1.00
I4 B:PYZ502 0.0 103.6 1.0
C4 B:PYZ502 2.1 77.7 1.0
C3 B:PYZ502 3.1 71.0 1.0
C5 B:PYZ502 3.1 72.5 1.0
I4 B:PYZ501 3.6 91.3 1.0
C4 B:PYZ501 3.6 102.5 1.0
CB B:LEU214 3.9 31.6 1.0
C5 B:PYZ501 4.0 96.0 1.0
CD2 B:LEU253 4.1 33.2 1.0
N2 B:PYZ502 4.2 76.4 1.0
C3 B:PYZ501 4.2 99.1 1.0
CA B:LEU214 4.2 32.6 1.0
N1 B:PYZ502 4.2 72.9 1.0
CG B:LEU253 4.2 32.9 1.0
CD1 B:LEU214 4.3 30.9 1.0
O B:MET210 4.3 41.1 1.0
N B:LEU214 4.4 35.5 1.0
CB B:LEU253 4.4 34.9 1.0
O B:HOH645 4.6 42.6 1.0
CB B:GLN254 4.6 36.4 1.0
N B:GLN254 4.6 36.3 1.0
CG B:LEU214 4.7 30.2 1.0
N1 B:PYZ501 4.7 94.2 1.0
N2 B:PYZ501 4.8 93.9 1.0
CA B:GLN254 4.8 35.5 1.0
C B:LEU253 4.9 35.6 1.0
CG B:GLN254 5.0 36.0 1.0

Iodine binding site 10 out of 16 in 9etb

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Iodine binding site 10 out of 16 in the CDK2-Cyclin A in Complex with Fraglite 2


Mono view


Stereo pair view

A full contact list of Iodine with other atoms in the I binding site number 10 of CDK2-Cyclin A in Complex with Fraglite 2 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:I503

b:143.5
occ:1.00
I4 B:PYZ503 0.0 143.5 1.0
C4 B:PYZ503 2.1 108.1 1.0
C5 B:PYZ503 3.1 96.7 1.0
C3 B:PYZ503 3.2 93.1 1.0
CD2 B:HIS296 3.5 71.6 1.0
CG B:HIS296 3.8 63.3 1.0
NE2 B:HIS296 3.8 80.1 1.0
CD1 A:LEU76 3.9 47.1 1.0
CG A:HIS71 4.1 90.4 1.0
CB A:HIS71 4.2 76.2 1.0
ND1 B:HIS296 4.2 66.7 1.0
CE1 B:HIS296 4.2 74.7 1.0
N1 B:PYZ503 4.3 93.3 1.0
N2 B:PYZ503 4.3 84.4 1.0
O B:HIS296 4.3 44.0 1.0
CA B:HIS296 4.3 46.7 1.0
CB B:HIS296 4.3 54.2 1.0
CD2 A:HIS71 4.4 92.2 1.0
CE2 B:PHE304 4.5 39.2 1.0
ND1 A:HIS71 4.6 96.3 1.0
CB B:LEU299 4.6 32.9 1.0
CD1 B:LEU299 4.7 32.1 1.0
CD2 A:LEU76 4.7 43.7 1.0
C B:HIS296 4.7 45.4 1.0
CZ B:PHE304 4.8 38.6 1.0
CG A:LEU76 4.9 45.9 1.0
CG2 A:VAL44 4.9 41.4 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: Sat Aug 9 00:43:42 2025

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