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Chlorine in PDB 4mq1: The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor

Enzymatic activity of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor

All present enzymatic activity of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor:
2.7.12.1;

Protein crystallography data

The structure of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor, PDB code: 4mq1 was solved by C.M.Lukacs, C.A.Janson, C.Garvie, L.Liang, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.83 / 2.35
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 263.843, 64.939, 140.461, 90.00, 115.16, 90.00
R / Rfree (%) 20.2 / 24.6

Chlorine Binding Sites:

The binding sites of Chlorine atom in the The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor (pdb code 4mq1). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 8 binding sites of Chlorine where determined in the The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor, PDB code: 4mq1:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Chlorine binding site 1 out of 8 in 4mq1

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Chlorine binding site 1 out of 8 in the The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:35.4
occ:1.00
 CL2 A:2C3501 0.0 35.4 1.0
C22 A:2C3501 1.7 28.9 1.0
C17 A:2C3501 2.7 28.1 1.0
C21 A:2C3501 2.7 26.9 1.0
N16 A:2C3501 2.7 29.8 1.0
O A:GLU239 3.1 43.1 1.0
O11 A:2C3501 3.5 37.6 1.0
CB A:PHE238 3.7 36.4 1.0
CG2 A:VAL222 3.9 34.9 1.0
CD1 A:LEU241 3.9 38.1 1.0
CG A:LEU241 3.9 38.2 1.0
C20 A:2C3501 4.0 27.3 1.0
C18 A:2C3501 4.0 28.4 1.0
CB A:ALA186 4.0 49.5 1.0
C14 A:2C3501 4.1 32.0 1.0
C A:GLU239 4.3 39.3 1.0
N A:LEU241 4.3 37.3 1.0
CG A:PHE238 4.4 34.9 1.0
CB A:LEU241 4.4 36.3 1.0
C19 A:2C3501 4.5 28.1 1.0
C10 A:2C3501 4.5 33.9 1.0
CA A:MET240 4.7 41.5 1.0
C12 A:2C3501 4.7 31.2 1.0
CG1 A:VAL306 4.7 34.9 1.0
CD2 A:LEU294 4.7 36.3 1.0
C A:MET240 4.8 41.2 1.0
CD2 A:PHE238 4.9 32.0 1.0
N A:MET240 4.9 38.7 1.0
C A:PHE238 5.0 37.5 1.0
O15 A:2C3501 5.0 34.2 1.0
CA A:LEU241 5.0 37.5 1.0

Chlorine binding site 2 out of 8 in 4mq1

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Chlorine binding site 2 out of 8 in the The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl501

b:53.8
occ:1.00
 CL3 A:2C3501 0.0 53.8 1.0
C33 A:2C3501 1.7 42.9 1.0
C32 A:2C3501 2.7 37.4 1.0
C35 A:2C3501 2.7 40.2 1.0
O A:HOH782 3.1 50.0 1.0
N A:GLY171 3.2 34.7 1.0
C A:GLY171 3.5 35.0 1.0
O A:GLY171 3.6 41.3 1.0
C A:PHE170 3.6 34.7 1.0
CB A:PHE170 3.6 38.1 1.0
CA A:GLY171 3.7 30.4 1.0
N A:PHE170 3.9 38.3 1.0
N A:GLN172 3.9 38.4 1.0
CA A:PHE170 3.9 37.0 1.0
C31 A:2C3501 3.9 34.0 1.0
C36 A:2C3501 3.9 38.5 1.0
CD A:LYS188 4.0 48.7 1.0
CG A:LYS188 4.0 47.7 1.0
O A:PHE170 4.2 37.6 1.0
CA A:GLY168 4.4 43.3 1.0
C37 A:2C3501 4.4 35.2 1.0
C A:GLY168 4.5 43.1 1.0
CA A:GLN172 4.5 36.8 1.0
O A:GLN172 4.6 34.0 1.0
N A:GLY168 4.6 49.8 1.0
O A:GLY168 4.6 42.6 1.0
C A:GLN172 4.7 35.6 1.0
CE A:LYS188 4.7 47.7 1.0
CG2 A:VAL173 4.9 40.7 1.0
CG A:PHE170 5.0 47.4 1.0
N A:SER169 5.0 41.1 1.0
O A:HOH601 5.0 45.5 1.0
NZ A:LYS188 5.0 46.3 1.0

Chlorine binding site 3 out of 8 in 4mq1

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Chlorine binding site 3 out of 8 in the The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:37.5
occ:1.00
 CL2 B:2C3501 0.0 37.5 1.0
C22 B:2C3501 1.7 33.2 1.0
C17 B:2C3501 2.6 34.0 1.0
C21 B:2C3501 2.7 33.0 1.0
N16 B:2C3501 2.7 33.5 1.0
O B:GLU239 3.1 39.9 1.0
O11 B:2C3501 3.3 39.9 1.0
CB B:PHE238 3.7 39.5 1.0
CB B:ALA186 3.8 44.4 1.0
C18 B:2C3501 3.9 32.4 1.0
C20 B:2C3501 4.0 32.5 1.0
C14 B:2C3501 4.0 32.0 1.0
CD1 B:LEU241 4.0 37.9 1.0
CG2 B:VAL222 4.1 40.0 1.0
CG B:LEU241 4.2 36.5 1.0
CG B:PHE238 4.3 37.0 1.0
C B:GLU239 4.3 39.2 1.0
C10 B:2C3501 4.4 33.8 1.0
C19 B:2C3501 4.5 30.5 1.0
N B:LEU241 4.5 43.0 1.0
C12 B:2C3501 4.6 35.3 1.0
CB B:LEU241 4.6 37.1 1.0
CG1 B:VAL306 4.6 32.8 1.0
CA B:MET240 4.7 40.1 1.0
CD2 B:PHE238 4.7 34.4 1.0
O15 B:2C3501 4.9 35.1 1.0
CD1 B:PHE238 4.9 34.3 1.0
C B:MET240 5.0 45.3 1.0
C B:PHE238 5.0 40.0 1.0

Chlorine binding site 4 out of 8 in 4mq1

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Chlorine binding site 4 out of 8 in the The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Cl501

b:51.5
occ:1.00
 CL3 B:2C3501 0.0 51.5 1.0
C33 B:2C3501 1.7 41.9 1.0
C35 B:2C3501 2.6 40.8 1.0
C32 B:2C3501 2.7 36.5 1.0
N B:GLY171 3.3 31.6 1.0
O B:HOH604 3.4 49.6 1.0
C B:GLY171 3.5 34.0 1.0
CD B:LYS188 3.5 42.7 1.0
CA B:GLY171 3.6 33.2 1.0
N B:GLN172 3.7 35.8 1.0
C B:PHE170 3.7 36.7 1.0
O B:GLY171 3.8 38.1 1.0
CB B:PHE170 3.9 45.0 1.0
C36 B:2C3501 3.9 40.2 1.0
C31 B:2C3501 3.9 34.8 1.0
CG B:LYS188 4.0 39.4 1.0
N B:PHE170 4.1 41.2 1.0
CA B:PHE170 4.1 41.3 1.0
O B:PHE170 4.3 36.4 1.0
C37 B:2C3501 4.4 36.3 1.0
CA B:GLN172 4.5 36.9 1.0
CA B:GLY168 4.6 43.7 1.0
O B:GLN172 4.6 38.3 1.0
C B:GLN172 4.7 36.4 1.0
C B:GLY168 4.7 44.3 1.0
CE B:LYS188 4.7 44.2 1.0
N B:GLY168 4.8 44.1 1.0
CG2 B:VAL173 4.9 37.2 1.0
O B:GLY168 5.0 42.4 1.0
NZ B:LYS188 5.0 45.6 1.0

Chlorine binding site 5 out of 8 in 4mq1

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Chlorine binding site 5 out of 8 in the The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:55.0
occ:1.00
 CL2 C:2C3501 0.0 55.0 1.0
C22 C:2C3501 1.7 63.8 1.0
C21 C:2C3501 2.7 60.5 1.0
C17 C:2C3501 2.7 59.8 1.0
N16 C:2C3501 2.8 61.5 1.0
O C:GLU239 3.1 50.3 1.0
O11 C:2C3501 3.5 61.1 1.0
CB C:PHE238 3.6 49.8 1.0
CB C:ALA186 3.8 51.5 1.0
CG2 C:VAL222 3.9 46.8 1.0
C20 C:2C3501 3.9 63.2 1.0
C18 C:2C3501 4.0 59.2 1.0
CG C:LEU241 4.0 61.7 1.0
C14 C:2C3501 4.1 64.5 1.0
CD1 C:LEU241 4.2 62.6 1.0
CG C:PHE238 4.3 49.6 1.0
C C:GLU239 4.3 51.6 1.0
N C:LEU241 4.3 56.0 1.0
CB C:LEU241 4.4 57.7 1.0
C19 C:2C3501 4.5 61.5 1.0
C10 C:2C3501 4.5 70.5 1.0
CG1 C:VAL306 4.7 46.2 1.0
C12 C:2C3501 4.8 67.0 1.0
C C:PHE238 4.8 49.3 1.0
CD1 C:PHE238 4.8 45.4 1.0
CD2 C:PHE238 4.8 48.6 1.0
CA C:MET240 4.9 58.6 1.0
CA C:PHE238 4.9 49.7 1.0
C C:MET240 4.9 56.3 1.0
O C:PHE238 5.0 46.2 1.0
N C:GLU239 5.0 51.8 1.0
CD2 C:LEU294 5.0 57.3 1.0

Chlorine binding site 6 out of 8 in 4mq1

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Chlorine binding site 6 out of 8 in the The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl501

b:60.9
occ:1.00
 CL3 C:2C3501 0.0 60.9 1.0
C33 C:2C3501 1.7 54.8 1.0
C32 C:2C3501 2.6 53.6 1.0
C35 C:2C3501 2.7 52.4 1.0
N C:GLY171 3.1 61.4 1.0
O C:GLY171 3.2 55.8 1.0
C C:GLY171 3.3 55.5 1.0
CA C:GLY171 3.6 56.6 1.0
C C:PHE170 3.8 61.8 1.0
CD C:LYS188 3.8 47.8 1.0
N C:GLN172 3.9 52.1 1.0
C31 C:2C3501 3.9 54.7 1.0
CG C:LYS188 3.9 46.8 1.0
C36 C:2C3501 4.0 55.5 1.0
CB C:PHE170 4.0 68.8 1.0
CA C:PHE170 4.2 62.6 1.0
CA C:GLY168 4.2 56.5 1.0
N C:PHE170 4.2 54.4 1.0
C C:GLY168 4.4 54.5 1.0
N C:GLY168 4.5 63.0 1.0
C37 C:2C3501 4.5 53.6 1.0
CA C:GLN172 4.5 52.7 1.0
O C:PHE170 4.6 60.9 1.0
O C:GLY168 4.6 53.6 1.0
C C:GLN172 4.6 56.6 1.0
O C:GLN172 4.6 63.8 1.0
CE C:LYS188 4.6 49.9 1.0
CG2 C:VAL173 4.8 48.0 1.0
C27 C:2C3501 5.0 54.9 1.0

Chlorine binding site 7 out of 8 in 4mq1

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Chlorine binding site 7 out of 8 in the The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:41.1
occ:1.00
 CL2 D:2C3501 0.0 41.1 1.0
C22 D:2C3501 1.8 46.9 1.0
C21 D:2C3501 2.8 44.3 1.0
C17 D:2C3501 2.8 42.9 1.0
N16 D:2C3501 2.9 42.0 1.0
O D:GLU239 3.0 47.7 1.0
O11 D:2C3501 3.4 45.6 1.0
CB D:PHE238 3.6 39.2 1.0
CB D:ALA186 3.9 42.9 1.0
CG2 D:VAL222 4.0 40.4 1.0
CG D:LEU241 4.0 52.7 1.0
C20 D:2C3501 4.1 46.3 1.0
C18 D:2C3501 4.1 45.0 1.0
CD1 D:LEU241 4.1 52.3 1.0
C D:GLU239 4.2 48.4 1.0
CG D:PHE238 4.2 39.7 1.0
C14 D:2C3501 4.2 43.2 1.0
N D:LEU241 4.3 43.9 1.0
C10 D:2C3501 4.5 50.1 1.0
CB D:LEU241 4.5 49.0 1.0
CD2 D:LEU294 4.6 44.7 1.0
C19 D:2C3501 4.6 47.0 1.0
C D:PHE238 4.7 44.4 1.0
CA D:MET240 4.8 47.0 1.0
CD1 D:PHE238 4.8 42.3 1.0
C12 D:2C3501 4.8 47.8 1.0
CA D:PHE238 4.8 38.8 1.0
CD2 D:PHE238 4.8 39.3 1.0
O D:PHE238 4.9 48.3 1.0
CG1 D:VAL306 4.9 37.2 1.0
C D:MET240 4.9 47.5 1.0
N D:MET240 4.9 48.9 1.0

Chlorine binding site 8 out of 8 in 4mq1

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Chlorine binding site 8 out of 8 in the The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Crystal Structure of DYRK1A with A Bound Pyrido[2,3-D]Pyrimidine Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Cl501

b:50.0
occ:1.00
 CL3 D:2C3501 0.0 50.0 1.0
C33 D:2C3501 1.7 39.5 1.0
C35 D:2C3501 2.6 40.8 1.0
C32 D:2C3501 2.7 36.6 1.0
N D:GLY171 2.9 36.3 1.0
C D:GLY171 3.3 37.0 1.0
O D:GLY171 3.3 40.5 1.0
CA D:GLY171 3.5 37.0 1.0
C D:PHE170 3.5 38.8 1.0
CD D:LYS188 3.7 37.0 1.0
CB D:PHE170 3.7 45.8 1.0
N D:GLN172 3.8 37.7 1.0
N D:PHE170 3.8 40.7 1.0
CA D:PHE170 3.9 41.8 1.0
C36 D:2C3501 3.9 39.8 1.0
C31 D:2C3501 4.0 36.8 1.0
CA D:GLY168 4.1 38.0 1.0
CG D:LYS188 4.1 35.8 1.0
N D:GLY168 4.3 41.3 1.0
C D:GLY168 4.3 36.5 1.0
O D:PHE170 4.3 39.9 1.0
C37 D:2C3501 4.4 40.6 1.0
O D:GLY168 4.5 38.8 1.0
CA D:GLN172 4.5 41.5 1.0
C D:GLN172 4.6 42.4 1.0
CE D:LYS188 4.7 38.1 1.0
O D:GLN172 4.8 39.6 1.0
N D:SER169 4.8 38.3 1.0
C D:SER169 5.0 42.0 1.0
NZ D:LYS188 5.0 39.3 1.0

Reference:

K.Anderson, Y.Chen, Z.Chen, R.Dominique, K.Glenn, Y.He, C.Janson, K.C.Luk, C.Lukacs, A.Polonskaia, Q.Qiao, A.Railkar, P.Rossman, H.Sun, Q.Xiang, M.Vilenchik, P.Wovkulich, X.Zhang. Pyrido[2,3-D]Pyrimidines: Discovery and Preliminary Sar of A Novel Series of DYRK1B and DYRK1A Inhibitors. Bioorg.Med.Chem.Lett. V. 23 6610 2013.
ISSN: ISSN 0960-894X
PubMed: 24239188
DOI: 10.1016/J.BMCL.2013.10.055
Page generated: Sun Jul 21 20:07:01 2024

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