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Fluorine in PDB 6b3e: Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor

Enzymatic activity of Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor

All present enzymatic activity of Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor:
2.7.11.22; 2.7.11.23;

Protein crystallography data

The structure of Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor, PDB code: 6b3e was solved by A.D.Ferguson, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 88.08 / 3.06
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 50.140, 77.260, 90.640, 76.53, 85.28, 78.22
R / Rfree (%) 19 / 21.2

Other elements in 6b3e:

The structure of Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor also contains other interesting chemical elements:

Magnesium (Mg) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor (pdb code 6b3e). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor, PDB code: 6b3e:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6b3e

Go back to Fluorine Binding Sites List in 6b3e
Fluorine binding site 1 out of 4 in the Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:69.4
occ:1.00
 F23 A:CJM1102 0.0 69.4 1.0
C22 A:CJM1102 1.3 65.4 1.0
C21 A:CJM1102 2.3 65.4 1.0
C16 A:CJM1102 2.4 63.3 1.0
F24 A:CJM1102 2.7 71.0 1.0
N15 A:CJM1102 3.0 60.4 1.0
O A:ILE733 3.5 82.7 1.0
C17 A:CJM1102 3.6 67.5 1.0
C20 A:CJM1102 3.6 60.4 1.0
OD2 A:ASP819 4.1 72.5 1.0
C19 A:CJM1102 4.1 62.3 1.0
C14 A:CJM1102 4.3 63.8 1.0
C A:ILE733 4.5 82.3 1.0
C27 A:CJM1102 4.5 56.7 1.0
N18 A:CJM1102 4.6 70.7 1.0
C26 A:CJM1102 4.6 55.2 1.0
CB A:ILE733 4.6 79.3 1.0
CA A:ILE733 4.7 76.3 1.0

Fluorine binding site 2 out of 4 in 6b3e

Go back to Fluorine Binding Sites List in 6b3e
Fluorine binding site 2 out of 4 in the Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F1102

b:71.0
occ:1.00
 F24 A:CJM1102 0.0 71.0 1.0
C21 A:CJM1102 1.3 65.4 1.0
C22 A:CJM1102 2.3 65.4 1.0
C20 A:CJM1102 2.3 60.4 1.0
F23 A:CJM1102 2.7 69.4 1.0
C19 A:CJM1102 3.6 62.3 1.0
C16 A:CJM1102 3.6 63.3 1.0
O A:ILE733 3.8 82.7 1.0
CA A:ILE733 3.9 76.3 1.0
C17 A:CJM1102 4.1 67.5 1.0
O A:ILE732 4.3 84.2 1.0
CB A:ILE733 4.3 79.3 1.0
C A:ILE733 4.3 82.3 1.0
CG2 A:ILE733 4.3 84.3 1.0
N15 A:CJM1102 4.9 60.4 1.0
N A:ILE733 5.0 76.8 1.0

Fluorine binding site 3 out of 4 in 6b3e

Go back to Fluorine Binding Sites List in 6b3e
Fluorine binding site 3 out of 4 in the Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1103

b:94.0
occ:1.00
 F23 C:CJM1103 0.0 94.0 1.0
C22 C:CJM1103 1.3 93.2 1.0
C21 C:CJM1103 2.4 92.9 1.0
C16 C:CJM1103 2.4 90.2 1.0
O C:ILE733 2.6 0.3 1.0
F24 C:CJM1103 2.7 93.6 1.0
N15 C:CJM1103 3.0 85.9 1.0
C17 C:CJM1103 3.6 92.1 1.0
C C:ILE733 3.6 0.1 1.0
C20 C:CJM1103 3.6 91.3 1.0
C27 C:CJM1103 3.9 72.7 1.0
CA C:ILE733 3.9 95.3 1.0
CB C:ILE733 4.0 98.4 1.0
C19 C:CJM1103 4.1 92.7 1.0
C28 C:CJM1103 4.3 74.2 1.0
C14 C:CJM1103 4.3 87.5 1.0
C26 C:CJM1103 4.5 73.0 1.0
N18 C:CJM1103 4.6 90.5 1.0
OD2 C:ASP819 4.6 96.0 1.0
CG2 C:ILE733 4.7 99.0 1.0
N C:GLY734 4.8 0.9 1.0

Fluorine binding site 4 out of 4 in 6b3e

Go back to Fluorine Binding Sites List in 6b3e
Fluorine binding site 4 out of 4 in the Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Crystal Structure of Human CDK12/Cyclink in Complex with An Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F1103

b:93.6
occ:1.00
 F24 C:CJM1103 0.0 93.6 1.0
C21 C:CJM1103 1.4 92.9 1.0
C22 C:CJM1103 2.4 93.2 1.0
C20 C:CJM1103 2.4 91.3 1.0
F23 C:CJM1103 2.7 94.0 1.0
C19 C:CJM1103 3.6 92.7 1.0
C16 C:CJM1103 3.6 90.2 1.0
CA C:ILE733 3.7 95.3 1.0
O C:ILE732 3.8 93.9 1.0
O C:ILE733 3.8 0.3 1.0
C17 C:CJM1103 4.1 92.1 1.0
C C:ILE733 4.2 0.1 1.0
CB C:ILE733 4.2 98.4 1.0
CG2 C:ILE733 4.3 99.0 1.0
C C:ILE732 4.7 94.7 1.0
N C:ILE733 4.7 94.3 1.0
N15 C:CJM1103 4.9 85.9 1.0

Reference:

J.W.Johannes, C.R.Denz, N.Su, A.Wu, A.C.Impastato, S.Mlynarski, J.G.Varnes, D.B.Prince, J.Cidado, N.Gao, M.Haddrick, N.H.Jones, S.Li, X.Li, Y.Liu, T.B.Nguyen, N.O'connell, E.Rivers, D.W.Robbins, R.Tomlinson, T.Yao, X.Zhu, A.D.Ferguson, M.L.Lamb, J.I.Manchester, S.Guichard. Structure-Based Design of Selective Noncovalent CDK12 Inhibitors. Chemmedchem V. 13 231 2018.
ISSN: ESSN 1860-7187
PubMed: 29266803
DOI: 10.1002/CMDC.201700695
Page generated: Thu Aug 1 17:57:36 2024

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