Bromine in PDB 7zh8: DYRK1A in Complex with A Bromo-Triazolo-Pyridine

Enzymatic activity of DYRK1A in Complex with A Bromo-Triazolo-Pyridine

All present enzymatic activity of DYRK1A in Complex with A Bromo-Triazolo-Pyridine:
2.7.12.1;

Protein crystallography data

The structure of DYRK1A in Complex with A Bromo-Triazolo-Pyridine, PDB code: 7zh8 was solved by M.Dammann, J.Stahlecker, T.Stehle, F.M.Boeckler, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.60 / 2.30
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 245.004, 64.663, 147.308, 90, 115.58, 90
R / Rfree (%) 19.9 / 23.5

Other elements in 7zh8:

The structure of DYRK1A in Complex with A Bromo-Triazolo-Pyridine also contains other interesting chemical elements:

Chlorine (Cl) 5 atoms

Bromine Binding Sites:

The binding sites of Bromine atom in the DYRK1A in Complex with A Bromo-Triazolo-Pyridine (pdb code 7zh8). This binding sites where shown within 5.0 Angstroms radius around Bromine atom.
In total 8 binding sites of Bromine where determined in the DYRK1A in Complex with A Bromo-Triazolo-Pyridine, PDB code: 7zh8:
Jump to Bromine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Bromine binding site 1 out of 8 in 7zh8

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Bromine binding site 1 out of 8 in the DYRK1A in Complex with A Bromo-Triazolo-Pyridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 1 of DYRK1A in Complex with A Bromo-Triazolo-Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br501

b:54.9
occ:1.00
 BR1 A:IWU501 0.0 54.9 1.0
C1 A:IWU501 1.9 48.1 1.0
C2 A:IWU501 2.8 39.8 1.0
C5 A:IWU501 2.9 45.0 1.0
O A:GLU239 3.3 46.0 1.0
CB A:PHE238 3.5 42.2 1.0
CD1 A:LEU241 3.7 40.5 1.0
CG2 A:VAL222 3.9 40.4 1.0
CG A:PHE238 4.0 40.8 1.0
CB A:ALA186 4.0 40.5 1.0
N1 A:IWU501 4.1 46.7 1.0
C4 A:IWU501 4.1 44.4 1.0
CG A:LEU241 4.1 53.1 1.0
CB A:LEU241 4.2 48.9 1.0
CD2 A:PHE238 4.4 42.6 1.0
CG1 A:VAL306 4.4 35.6 1.0
C A:GLU239 4.5 51.5 1.0
C3 A:IWU501 4.5 42.8 1.0
N A:LEU241 4.6 55.4 1.0
CD1 A:PHE238 4.7 38.8 1.0
CD2 A:LEU294 4.7 45.4 1.0
CA A:PHE238 4.9 41.2 1.0

Bromine binding site 2 out of 8 in 7zh8

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Bromine binding site 2 out of 8 in the DYRK1A in Complex with A Bromo-Triazolo-Pyridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 2 of DYRK1A in Complex with A Bromo-Triazolo-Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Br503

b:74.0
occ:1.00
 BR1 A:IWU503 0.0 74.0 1.0
C1 A:IWU503 1.9 45.8 1.0
C5 A:IWU503 2.9 44.0 1.0
C2 A:IWU503 2.9 38.4 1.0
O A:HOH667 3.4 43.2 1.0
O A:HOH654 3.6 47.3 1.0
O C:HOH635 3.6 52.0 1.0
CD2 A:LEU377 3.8 31.9 1.0
O A:VAL376 4.0 34.9 1.0
C4 A:IWU503 4.1 46.9 1.0
N1 A:IWU503 4.1 44.4 1.0
CA A:LEU377 4.2 35.9 1.0
C1 C:PEG501 4.2 48.2 1.0
O1 C:PEG501 4.2 56.3 1.0
O A:LEU377 4.2 31.1 1.0
CD2 A:LEU457 4.5 36.5 1.0
NH1 C:ARG458 4.5 55.9 1.0
C3 A:IWU503 4.6 44.5 1.0
C A:LEU377 4.6 38.6 1.0
CB A:LEU377 4.8 35.5 1.0
NH2 C:ARG458 4.9 50.5 1.0
C A:VAL376 4.9 38.8 1.0
CG A:LEU377 4.9 37.2 1.0

Bromine binding site 3 out of 8 in 7zh8

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Bromine binding site 3 out of 8 in the DYRK1A in Complex with A Bromo-Triazolo-Pyridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 3 of DYRK1A in Complex with A Bromo-Triazolo-Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br501

b:55.9
occ:1.00
 BR1 B:IWU501 0.0 55.9 1.0
C1 B:IWU501 1.9 53.2 1.0
C2 B:IWU501 2.8 50.6 1.0
C5 B:IWU501 2.9 46.6 1.0
O B:GLU239 3.3 53.4 1.0
CB B:PHE238 3.6 45.6 1.0
CB B:ALA186 3.8 50.5 1.0
CG B:PHE238 4.0 44.4 1.0
CG2 B:VAL222 4.0 47.3 1.0
CD1 B:LEU241 4.1 48.2 1.0
N1 B:IWU501 4.1 56.1 1.0
C4 B:IWU501 4.1 49.4 1.0
CB B:LEU241 4.3 59.2 1.0
CG B:LEU241 4.4 55.9 1.0
CD1 B:PHE238 4.4 45.5 1.0
CG1 B:VAL306 4.5 45.7 1.0
CD2 B:LEU294 4.5 53.6 1.0
C B:GLU239 4.5 55.7 1.0
C3 B:IWU501 4.6 52.3 1.0
CD2 B:PHE238 4.7 43.8 1.0
N B:LEU241 4.7 66.5 1.0
O B:HOH651 4.8 69.7 1.0
CA B:PHE238 4.9 47.4 1.0

Bromine binding site 4 out of 8 in 7zh8

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Bromine binding site 4 out of 8 in the DYRK1A in Complex with A Bromo-Triazolo-Pyridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 4 of DYRK1A in Complex with A Bromo-Triazolo-Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Br502

b:75.8
occ:1.00
 BR1 B:IWU502 0.0 75.8 1.0
C1 B:IWU502 1.9 46.4 1.0
C5 B:IWU502 2.8 40.7 1.0
C2 B:IWU502 2.9 40.3 1.0
CD2 B:LEU377 3.9 33.3 1.0
C4 B:IWU502 4.1 43.0 1.0
N1 B:IWU502 4.1 42.9 1.0
CA B:LEU377 4.2 38.3 1.0
CD2 B:LEU457 4.2 39.2 1.0
O B:VAL376 4.2 39.6 1.0
O B:LEU377 4.5 43.4 1.0
C3 B:IWU502 4.6 45.5 1.0
O B:HOH670 4.6 43.6 1.0
CB B:LEU377 4.7 34.0 1.0
C B:LEU377 4.7 40.1 1.0
CG B:LEU377 4.9 38.9 1.0

Bromine binding site 5 out of 8 in 7zh8

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Bromine binding site 5 out of 8 in the DYRK1A in Complex with A Bromo-Triazolo-Pyridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 5 of DYRK1A in Complex with A Bromo-Triazolo-Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br502

b:88.3
occ:1.00
 BR1 C:IWU502 0.0 88.3 1.0
C1 C:IWU502 1.9 61.0 1.0
C2 C:IWU502 2.9 66.7 1.0
C5 C:IWU502 2.9 60.6 1.0
O C:GLU239 3.5 88.7 1.0
CB C:PHE238 3.6 76.9 1.0
O C:HOH660 3.7 80.8 1.0
CD1 C:LEU241 4.0 72.6 1.0
CG2 C:VAL222 4.1 68.8 1.0
C4 C:IWU502 4.1 64.6 1.0
N1 C:IWU502 4.1 66.3 1.0
CG C:PHE238 4.1 75.2 1.0
CD2 C:LEU294 4.3 69.1 1.0
CB C:ALA186 4.3 85.2 1.0
CG1 C:VAL306 4.3 61.4 1.0
CD2 C:PHE238 4.6 71.1 1.0
C3 C:IWU502 4.6 68.2 1.0
C C:GLU239 4.7 89.7 1.0
CG C:LEU241 4.7 85.0 1.0
CD1 C:PHE238 4.8 71.5 1.0
CB C:LEU241 4.8 82.3 1.0
CA C:PHE238 5.0 82.5 1.0

Bromine binding site 6 out of 8 in 7zh8

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Bromine binding site 6 out of 8 in the DYRK1A in Complex with A Bromo-Triazolo-Pyridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 6 of DYRK1A in Complex with A Bromo-Triazolo-Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Br504

b:93.7
occ:1.00
 BR1 C:IWU504 0.0 93.7 1.0
C1 C:IWU504 1.9 63.5 1.0
C2 C:IWU504 2.8 53.9 1.0
C5 C:IWU504 2.8 60.0 1.0
O C:HOH633 3.3 58.8 1.0
CD2 C:LEU377 3.9 44.8 1.0
O C:VAL376 4.1 53.0 1.0
C4 C:IWU504 4.1 60.5 1.0
N1 C:IWU504 4.1 59.1 1.0
O4 C:PEG505 4.3 69.2 1.0
CA C:LEU377 4.3 47.4 1.0
CD2 C:LEU457 4.4 46.7 1.0
C3 C:IWU504 4.6 61.2 1.0
NH1 A:ARG458 4.6 57.2 1.0
O C:LEU377 4.7 52.4 1.0
C C:LEU377 4.8 53.0 1.0
CD1 C:LEU457 4.9 44.2 1.0
O C:HOH646 4.9 51.2 1.0
CB C:LEU377 4.9 48.6 1.0
C4 C:PEG505 4.9 61.0 1.0
C C:VAL376 5.0 52.1 1.0

Bromine binding site 7 out of 8 in 7zh8

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Bromine binding site 7 out of 8 in the DYRK1A in Complex with A Bromo-Triazolo-Pyridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 7 of DYRK1A in Complex with A Bromo-Triazolo-Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br501

b:75.5
occ:1.00
 BR1 D:IWU501 0.0 75.5 1.0
C1 D:IWU501 1.9 77.7 1.0
C2 D:IWU501 2.8 62.5 1.0
C5 D:IWU501 2.9 64.1 1.0
O D:GLU239 3.3 65.4 1.0
CD1 D:LEU241 3.5 61.8 1.0
CB D:PHE238 3.6 67.6 1.0
CG D:LEU241 4.0 72.6 1.0
CB D:ALA186 4.1 69.4 1.0
CG D:PHE238 4.1 68.7 1.0
N1 D:IWU501 4.1 71.3 1.0
CG2 D:VAL222 4.1 66.2 1.0
C4 D:IWU501 4.1 71.9 1.0
CG1 D:VAL306 4.3 62.9 1.0
CB D:LEU241 4.4 64.1 1.0
C D:GLU239 4.5 74.6 1.0
CD1 D:PHE238 4.5 68.2 1.0
C3 D:IWU501 4.6 71.4 1.0
CD2 D:LEU294 4.6 66.4 1.0
N D:LEU241 4.7 71.6 1.0
CD2 D:PHE238 4.8 68.5 1.0
CA D:PHE238 4.9 68.9 1.0

Bromine binding site 8 out of 8 in 7zh8

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Bromine binding site 8 out of 8 in the DYRK1A in Complex with A Bromo-Triazolo-Pyridine


Mono view


Stereo pair view

A full contact list of Bromine with other atoms in the Br binding site number 8 of DYRK1A in Complex with A Bromo-Triazolo-Pyridine within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Br502

b:95.4
occ:1.00
 BR1 D:IWU502 0.0 95.4 1.0
C1 D:IWU502 1.9 66.4 1.0
C5 D:IWU502 2.8 59.9 1.0
C2 D:IWU502 2.8 57.1 1.0
CD2 D:LEU377 3.9 59.1 1.0
O D:VAL376 4.0 59.5 1.0
CA D:LEU377 4.0 55.4 1.0
CD2 D:LEU457 4.0 59.2 1.0
C4 D:IWU502 4.1 66.6 1.0
N1 D:IWU502 4.1 60.8 1.0
O D:LEU377 4.3 59.1 1.0
C D:LEU377 4.5 59.0 1.0
CB D:LEU377 4.5 53.2 1.0
C3 D:IWU502 4.6 67.0 1.0
C D:VAL376 4.8 56.4 1.0
N D:LEU377 4.9 53.6 1.0
CG D:LEU377 4.9 54.9 1.0

Reference:

M.Dammann, J.Stahlecker, M.O.Zimmermann, T.Klett, K.Rotzinger, M.Kramer, M.Coles, T.Stehle, F.M.Boeckler. Screening of A Halogen-Enriched Fragment Library Leads to Unconventional Binding Modes. J.Med.Chem. V. 65 14539 2022.
ISSN: ISSN 0022-2623
PubMed: 36288453
DOI: 10.1021/ACS.JMEDCHEM.2C00951
Page generated: Thu Jul 11 04:48:20 2024

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