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Iodine in PDB 9et8: CDK2-Cyclin A in Complex with Fraglite 5

Enzymatic activity of CDK2-Cyclin A in Complex with Fraglite 5

All present enzymatic activity of CDK2-Cyclin A in Complex with Fraglite 5:
2.7.11.22;

Protein crystallography data

The structure of CDK2-Cyclin A in Complex with Fraglite 5, PDB code: 9et8 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) 99.04 / 2.31
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 74.171, 133.268, 147.371, 90, 90, 90
R / Rfree (%) 22.5 / 24.2

Iodine Binding Sites:

The binding sites of Iodine atom in the CDK2-Cyclin A in Complex with Fraglite 5 (pdb code 9et8). This binding sites where shown within 5.0 Angstroms radius around Iodine atom.
In total 7 binding sites of Iodine where determined in the CDK2-Cyclin A in Complex with Fraglite 5, PDB code: 9et8:
Jump to Iodine binding site number: 1; 2; 3; 4; 5; 6; 7;

Iodine binding site 1 out of 7 in 9et8

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Iodine binding site 1 out of 7 in the CDK2-Cyclin A in Complex with Fraglite 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I601

b:61.3
occ:1.00
 I1 A:IIS601 0.0 61.3 1.0
C3 A:IIS601 2.1 53.8 1.0
C2 A:IIS601 3.1 49.4 1.0
C4 A:IIS601 3.1 56.0 1.0
CZ A:PHE109 4.2 45.4 1.0
CE2 A:PHE109 4.3 43.9 1.0
C5 A:IIS601 4.4 56.7 1.0
C1 A:IIS601 4.4 51.7 1.0
O A:PHE286 4.7 50.7 1.0
N2 A:IIS601 4.9 52.8 1.0

Iodine binding site 2 out of 7 in 9et8

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Iodine binding site 2 out of 7 in the CDK2-Cyclin A in Complex with Fraglite 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I602

b:129.1
occ:0.50
 I1 A:IIS602 0.0 129.1 0.5
C3 A:IIS602 2.1 91.7 0.5
C2 A:IIS602 2.7 44.0 0.5
C4 A:IIS602 3.0 77.1 0.5
C2 A:IIS602 3.1 81.0 0.5
C1 A:IIS602 3.6 42.0 0.5
N1 A:IIS602 3.6 41.5 0.5
C3 A:IIS602 3.7 45.2 0.5
I1 A:IIS602 4.0 52.0 0.5
CG1 A:VAL18 4.3 53.6 1.0
C5 A:IIS602 4.3 68.3 0.5
C1 A:IIS602 4.4 71.3 0.5
CB A:VAL18 4.7 55.3 1.0
O A:ILE10 4.7 62.9 1.0
CD1 A:ILE10 4.8 56.9 1.0
CG2 A:VAL18 4.8 52.8 1.0
CD2 A:LEU134 4.8 43.1 1.0
N2 A:IIS602 4.8 41.0 0.5
N2 A:IIS602 4.9 66.2 0.5
CG1 A:ILE10 4.9 60.6 1.0
CA A:GLY11 4.9 61.3 1.0
C4 A:IIS602 5.0 42.3 0.5

Iodine binding site 3 out of 7 in 9et8

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Iodine binding site 3 out of 7 in the CDK2-Cyclin A in Complex with Fraglite 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I602

b:52.0
occ:0.50
 I1 A:IIS602 0.0 52.0 0.5
C3 A:IIS602 2.1 45.2 0.5
C2 A:IIS602 2.5 81.0 0.5
O A:HOH791 2.7 57.6 1.0
C2 A:IIS602 3.0 44.0 0.5
C4 A:IIS602 3.0 42.3 0.5
C1 A:IIS602 3.3 71.3 0.5
N1 A:IIS602 3.4 64.1 0.5
C3 A:IIS602 3.5 91.7 0.5
I1 A:IIS602 4.0 129.1 0.5
CD2 A:PHE80 4.2 43.1 1.0
C5 A:IIS602 4.3 40.4 0.5
C1 A:IIS602 4.3 42.0 0.5
CE2 A:PHE80 4.4 42.2 1.0
CG1 A:VAL18 4.4 53.6 1.0
CE A:LYS33 4.5 55.6 1.0
CG2 A:VAL18 4.6 52.8 1.0
N2 A:IIS602 4.6 66.2 0.5
C4 A:IIS602 4.8 77.1 0.5
N2 A:IIS602 4.8 41.0 0.5
CD A:LYS33 4.9 53.1 1.0
CG A:PHE80 4.9 42.5 1.0
CB A:LYS33 5.0 51.5 1.0

Iodine binding site 4 out of 7 in 9et8

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Iodine binding site 4 out of 7 in the CDK2-Cyclin A in Complex with Fraglite 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:I603

b:153.5
occ:1.00
 I1 A:IIS603 0.0 153.5 1.0
C3 A:IIS603 2.1 134.2 1.0
C2 A:IIS603 3.0 124.2 1.0
C4 A:IIS603 3.1 128.5 1.0
CD2 A:TYR19 3.7 73.3 1.0
CG A:TYR19 3.8 70.8 1.0
CB A:LYS6 3.8 70.5 1.0
CD A:LYS6 3.9 91.5 1.0
CD1 A:LEU32 3.9 52.6 1.0
CB A:TYR19 4.0 63.6 1.0
CE2 A:TYR19 4.2 82.4 1.0
CG A:LYS6 4.3 84.5 1.0
C1 A:IIS603 4.4 131.8 1.0
C5 A:IIS603 4.4 131.2 1.0
CD1 A:TYR19 4.4 76.7 1.0
CE A:LYS6 4.5 95.5 1.0
CE1 A:TYR77 4.5 70.0 1.0
NZ A:LYS6 4.6 89.0 1.0
CZ A:TYR19 4.8 93.4 1.0
CB A:LEU32 4.9 50.3 1.0
CE1 A:TYR19 4.9 87.7 1.0
N2 A:IIS603 4.9 136.1 1.0
CE A:MET1 4.9 75.6 1.0

Iodine binding site 5 out of 7 in 9et8

Go back to Iodine Binding Sites List in 9et8
Iodine binding site 5 out of 7 in the CDK2-Cyclin A in Complex with Fraglite 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I301

b:80.7
occ:1.00
 I1 C:IIS301 0.0 80.7 1.0
C3 C:IIS301 2.1 54.9 1.0
C2 C:IIS301 3.0 50.9 1.0
C4 C:IIS301 3.0 47.7 1.0
O C:HOH438 3.3 48.7 1.0
O C:HOH402 3.4 52.3 1.0
C5 C:IIS301 4.3 48.4 1.0
C1 C:IIS301 4.3 47.0 1.0
CD2 C:PHE80 4.4 41.4 1.0
CG1 C:VAL18 4.4 53.5 1.0
CE2 C:PHE80 4.5 40.6 1.0
CG C:PHE80 4.6 40.1 1.0
CD1 C:LEU134 4.7 42.7 1.0
NZ C:LYS33 4.8 63.9 1.0
N2 C:IIS301 4.8 47.5 1.0
CG2 C:VAL18 4.8 56.4 1.0
CZ C:PHE80 4.9 40.1 1.0
CD1 C:PHE80 5.0 39.9 1.0

Iodine binding site 6 out of 7 in 9et8

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Iodine binding site 6 out of 7 in the CDK2-Cyclin A in Complex with Fraglite 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I302

b:96.5
occ:1.00
 I1 C:IIS302 0.0 96.5 1.0
C3 C:IIS302 2.1 87.7 1.0
C2 C:IIS302 3.1 78.8 1.0
C4 C:IIS302 3.1 78.1 1.0
CD1 C:TYR19 3.4 64.4 1.0
CG C:TYR19 3.5 63.2 1.0
CG C:LYS6 3.6 71.8 1.0
CE1 C:TYR19 3.7 72.3 1.0
CD C:LYS6 3.9 77.3 1.0
CD2 C:TYR19 4.0 66.8 1.0
CB C:TYR19 4.0 56.7 1.0
CE1 C:TYR77 4.1 56.8 1.0
CD1 C:LEU32 4.1 45.7 1.0
CZ C:TYR19 4.2 77.8 1.0
CE2 C:TYR19 4.2 72.7 1.0
C5 C:IIS302 4.4 79.8 1.0
C1 C:IIS302 4.4 81.4 1.0
CB C:LEU32 4.5 44.5 1.0
NZ C:LYS34 4.7 78.7 1.0
CD1 C:TYR77 4.7 54.6 1.0
CE C:LYS34 4.7 76.3 1.0
CE C:LYS6 4.9 78.7 1.0
N2 C:IIS302 4.9 81.2 1.0
CG C:LEU32 5.0 44.6 1.0

Iodine binding site 7 out of 7 in 9et8

Go back to Iodine Binding Sites List in 9et8
Iodine binding site 7 out of 7 in the CDK2-Cyclin A in Complex with Fraglite 5


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 5 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:I303

b:111.2
occ:1.00
 I1 C:IIS303 0.0 111.2 1.0
C3 C:IIS303 2.1 96.0 1.0
C2 C:IIS303 3.1 89.0 1.0
C4 C:IIS303 3.1 88.3 1.0
CD C:ARG217 3.8 65.4 1.0
NE1 C:TRP243 4.0 73.7 1.0
CZ2 C:TRP243 4.3 73.9 1.0
C5 C:IIS303 4.4 84.4 1.0
C1 C:IIS303 4.4 85.6 1.0
CG C:ARG217 4.5 66.5 1.0
CE2 C:TRP243 4.5 73.7 1.0
NH1 C:ARG217 4.8 66.5 1.0
NE C:ARG217 4.8 65.6 1.0
N2 C:IIS303 4.9 81.8 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 00:43:29 2025

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