Chlorine in PDB 7vds: The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24

Enzymatic activity of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24

All present enzymatic activity of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24:
2.7.11.1;

Protein crystallography data

The structure of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24, PDB code: 7vds was solved by G.Malojcic, S.L.Clugston, M.Daniels, J.C.Harmange, M.Ledeborer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.51 / 3.05
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.06, 118.06, 153.69, 90, 90, 120
R / Rfree (%) 22.5 / 27.2

Other elements in 7vds:

The structure of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 also contains other interesting chemical elements:

Fluorine (F) 1 atom

Chlorine Binding Sites:

Pages:

>>> Page 1 <<< Page 2, Binding sites: 11 - 19;

Binding sites:

The binding sites of Chlorine atom in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 (pdb code 7vds). This binding sites where shown within 5.0 Angstroms radius around Chlorine atom.
In total 19 binding sites of Chlorine where determined in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24, PDB code: 7vds:
Jump to Chlorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8; 9; 10;

Chlorine binding site 1 out of 19 in 7vds

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Chlorine binding site 1 out of 19 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 1 of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl318

b:108.8
occ:1.00
 O A:GLY138 3.8 104.2 1.0
C A:GLY138 4.2 111.0 1.0
CG A:GLU139 4.3 115.0 1.0
O A:ASN137 4.4 108.1 1.0
NE2 A:GLN109 4.4 105.4 1.0
OE1 A:GLN109 4.4 94.4 1.0
N A:GLU139 4.5 115.5 1.0
CA A:GLU139 4.6 109.0 1.0
CD A:GLN109 4.6 96.2 1.0
OG A:SER105 4.7 106.7 1.0
CA A:GLY138 5.0 106.0 1.0

Chlorine binding site 2 out of 19 in 7vds

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Chlorine binding site 2 out of 19 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 2 of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl319

b:116.5
occ:1.00
 O A:GLN273 3.9 99.6 1.0
O A:VAL272 4.0 91.5 1.0
OE1 A:GLU279 4.2 125.4 1.0
C A:GLN273 4.2 93.3 1.0
O A:ARG274 4.3 99.5 1.0
CA A:GLN273 4.4 103.5 1.0
C A:ARG274 4.8 88.3 1.0
OE2 A:GLU279 4.9 132.3 1.0
C A:VAL272 5.0 93.3 1.0
CD A:GLU279 5.0 126.3 1.0

Chlorine binding site 3 out of 19 in 7vds

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Chlorine binding site 3 out of 19 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 3 of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl320

b:135.4
occ:1.00
 O A:GLU12 3.7 170.4 1.0
N A:GLU12 4.3 154.5 1.0
C A:GLU12 4.4 168.6 1.0
CA A:GLU12 4.8 157.6 1.0
CB A:GLU12 4.8 162.1 1.0

Chlorine binding site 4 out of 19 in 7vds

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Chlorine binding site 4 out of 19 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 4 of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl321

b:136.2
occ:1.00
 NZ A:LYS128 2.9 102.7 1.0
OD2 A:ASP144 3.0 110.8 1.0
OD2 A:ASP126 3.4 106.4 1.0
CE A:LYS128 3.7 100.5 1.0
O A:HOH417 3.9 107.9 1.0
C1 A:61U301 4.1 84.0 1.0
ND2 A:ASN131 4.2 82.5 1.0
CG A:ASP144 4.2 104.3 1.0
OD1 A:ASN131 4.3 90.0 1.0
CG A:ASP126 4.4 106.6 1.0
OD1 A:ASP126 4.6 106.5 1.0
CG A:ASN131 4.7 87.6 1.0
N1 A:61U301 4.8 81.0 1.0
OD1 A:ASP144 4.9 106.5 1.0

Chlorine binding site 5 out of 19 in 7vds

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Chlorine binding site 5 out of 19 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 5 of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl322

b:136.6
occ:1.00
 O2 A:GOL303 2.9 120.8 1.0
O A:HOH412 3.0 73.1 1.0
O A:LYS56 3.7 98.2 1.0
CD A:LYS59 3.9 100.9 1.0
OE1 A:GLU57 4.0 121.4 1.0
CA A:GLU57 4.0 90.8 1.0
CG A:LYS59 4.0 93.3 1.0
C2 A:GOL303 4.1 128.5 1.0
C1 A:GOL303 4.3 128.1 1.0
CE A:LYS59 4.3 102.1 1.0
C A:GLU57 4.3 89.2 1.0
O A:GLU57 4.4 85.8 1.0
CB A:LYS59 4.6 86.6 1.0
C A:LYS56 4.6 84.2 1.0
O A:HOH414 4.7 80.7 1.0
O A:HOH409 4.8 79.5 1.0
N A:GLU57 4.8 81.9 1.0
CD A:GLU57 4.9 109.4 1.0

Chlorine binding site 6 out of 19 in 7vds

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Chlorine binding site 6 out of 19 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 6 of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl323

b:129.1
occ:1.00
 O A:ILE29 2.9 92.0 1.0
N A:PHE82 3.3 102.5 1.0
OE2 A:GLU28 3.8 146.8 1.0
CA A:GLU81 3.9 89.8 1.0
C A:GLU81 4.1 91.7 1.0
C A:ILE29 4.1 97.7 1.0
CB A:GLU81 4.1 93.4 1.0
O A:PHE82 4.2 101.5 1.0
CB A:PHE82 4.3 103.2 1.0
CA A:PHE82 4.3 102.2 1.0
CD A:GLU28 4.4 133.8 1.0
CG A:GLU28 4.5 129.2 1.0
CA A:VAL30 4.7 96.8 1.0
CG1 A:VAL30 4.7 99.5 1.0
C A:PHE82 4.8 105.9 1.0
N A:VAL30 4.8 94.8 1.0
NE2 A:HIS67 4.8 77.5 1.0
CG1 A:ILE29 4.9 120.4 1.0

Chlorine binding site 7 out of 19 in 7vds

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Chlorine binding site 7 out of 19 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 7 of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl324

b:133.0
occ:1.00
 O1 A:EDO309 4.5 133.1 1.0

Chlorine binding site 8 out of 19 in 7vds

Go back to Chlorine Binding Sites List in 7vds
Chlorine binding site 8 out of 19 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 8 of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl325

b:125.6
occ:1.00
 OH A:TYR158 3.1 103.7 1.0
O A:ILE153 3.8 107.8 1.0
CZ A:TYR158 3.9 94.6 1.0
N A:VAL155 4.2 100.5 1.0
CG2 A:VAL155 4.3 100.0 1.0
CD2 A:LEU178 4.4 113.5 1.0
CE2 A:TYR158 4.5 93.6 1.0
CA A:PRO154 4.5 117.1 1.0
CE1 A:TYR158 4.7 98.0 1.0
C A:ILE153 4.7 101.0 1.0
O A:VAL155 4.8 108.8 1.0
C A:PRO154 4.8 106.8 1.0

Chlorine binding site 9 out of 19 in 7vds

Go back to Chlorine Binding Sites List in 7vds
Chlorine binding site 9 out of 19 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 9 of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl326

b:94.1
occ:1.00
 SG A:CYS269 3.6 94.8 1.0
N A:CYS269 3.9 90.5 1.0
CB A:CYS269 4.1 94.2 1.0
NE2 A:GLN226 4.4 114.2 1.0
O A:LEU267 4.5 96.3 1.0
CB A:LEU219 4.6 82.3 1.0
O A:GLY220 4.6 80.0 1.0
O A:LEU219 4.6 82.5 1.0
CA A:LYS268 4.6 93.1 1.0
CA A:CYS269 4.7 89.1 1.0
CG A:PRO222 4.7 86.9 1.0
C A:LYS268 4.8 90.1 1.0

Chlorine binding site 10 out of 19 in 7vds

Go back to Chlorine Binding Sites List in 7vds
Chlorine binding site 10 out of 19 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24


Mono view


Stereo pair view

A full contact list of Chlorine with other atoms in the Cl binding site number 10 of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 24 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl327

b:111.5
occ:1.00
 OG A:SER229 3.5 111.8 1.0
NE1 A:TRP227 3.7 86.9 1.0
CB A:SER229 3.9 112.4 1.0
CG A:PRO271 4.0 83.1 1.0
CD2 A:LEU233 4.1 96.7 1.0
C1 A:EDO317 4.1 137.3 1.0
CD A:PRO271 4.4 81.9 1.0
CE2 A:TRP227 4.4 84.1 1.0
CZ2 A:TRP227 4.4 83.8 1.0
CD1 A:LEU233 4.7 97.2 1.0
CG A:LEU233 4.7 94.8 1.0
CD1 A:TRP227 4.7 87.9 1.0
O1 A:EDO317 4.8 144.5 1.0
CB A:ASP171 4.8 84.2 1.0

Reference:

M.H.Daniels, G.Malojcic, S.L.Clugston, B.Williams, M.Coeffet-Le Gal, X.R.Pan-Zhou, S.Venkatachalan, J.C.Harmange, M.Ledeboer. Discovery and Optimization of Highly Selective Inhibitors of CDK5. J.Med.Chem. V. 65 3575 2022.
ISSN: ISSN 0022-2623
PubMed: 35143203
DOI: 10.1021/ACS.JMEDCHEM.1C02069
Page generated: Tue Apr 4 22:06:04 2023

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