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Chlorine in PDB 7vdp: The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1

Enzymatic activity of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1

All present enzymatic activity of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1:
2.7.11.1;

Protein crystallography data

The structure of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1, PDB code: 7vdp 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) 51.79 / 2.09
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 118.37, 118.37, 155.37, 90, 90, 120
R / Rfree (%) 20.1 / 22.9

Other elements in 7vdp:

The structure of The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1 also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Chlorine Binding Sites:

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

Chlorine binding site 1 out of 7 in 7vdp

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Chlorine binding site 1 out of 7 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl311

b:44.4
occ:1.00
 NZ A:LYS213 3.1 45.9 1.0
O A:HOH511 3.1 30.0 1.0
O A:HOH434 3.3 52.4 1.0
CE A:LYS213 3.7 43.9 1.0
NZ A:LYS237 3.9 53.3 1.0
OD2 A:ASP209 4.0 48.5 1.0
OD1 A:ASP209 4.5 45.4 1.0
CG A:ASP209 4.6 45.6 1.0
CE A:LYS237 4.8 50.6 1.0
O A:HOH534 4.9 45.1 1.0

Chlorine binding site 2 out of 7 in 7vdp

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Chlorine binding site 2 out of 7 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl312

b:63.3
occ:1.00
 OE1 A:GLU51 2.8 38.1 1.0
N A:ASP144 2.9 33.0 1.0
O A:HOH453 3.0 48.4 1.0
CA A:ASP144 3.4 33.6 1.0
CZ A:PHE80 3.5 33.1 1.0
CE2 A:PHE80 3.6 32.6 1.0
CG1 A:VAL64 3.7 33.6 1.0
C25 A:65L301 3.9 35.0 1.0
O18 A:65L301 3.9 38.2 1.0
CD A:GLU51 3.9 37.9 1.0
C A:ALA143 3.9 32.2 1.0
CB A:ALA143 4.0 31.5 1.0
CA A:ALA143 4.1 31.8 1.0
CE1 A:PHE80 4.2 34.6 1.0
C17 A:65L301 4.3 37.3 1.0
CB A:ASP144 4.4 35.5 1.0
OE2 A:GLU51 4.4 40.0 1.0
CD2 A:PHE80 4.4 31.7 1.0
N A:PHE145 4.4 32.1 1.0
C A:ASP144 4.4 33.5 1.0
CD1 A:LEU55 4.6 35.1 1.0
C19 A:65L301 4.7 39.7 1.0
C20 A:65L301 4.8 39.8 1.0
CB A:VAL64 4.8 31.4 1.0
C26 A:65L301 4.9 33.9 1.0
CG2 A:VAL64 4.9 33.3 1.0
C24 A:65L301 4.9 40.6 1.0
CD1 A:PHE80 5.0 34.4 1.0

Chlorine binding site 3 out of 7 in 7vdp

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Chlorine binding site 3 out of 7 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl313

b:54.8
occ:1.00
 OH A:TYR4 2.8 48.3 1.0
ND2 A:ASN23 3.3 53.2 1.0
O A:HOH452 3.5 48.3 1.0
CZ A:TYR4 3.7 47.3 1.0
CE2 A:TYR4 3.8 45.7 1.0
CG1 A:VAL30 3.8 42.9 1.0
CG1 A:VAL79 4.2 37.8 1.0
CB A:ASN23 4.3 51.6 1.0
CG A:ASN23 4.3 53.0 1.0
OE1 A:GLU28 4.4 59.5 1.0
CB A:VAL30 5.0 41.7 1.0

Chlorine binding site 4 out of 7 in 7vdp

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Chlorine binding site 4 out of 7 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl314

b:64.3
occ:1.00
 O A:HOH506 2.6 51.7 1.0
O A:HOH532 3.1 43.6 1.0
N A:CYS269 3.1 32.7 1.0
SG A:CYS269 3.6 36.5 1.0
CB A:CYS269 3.7 36.7 1.0
CA A:LYS268 3.9 36.0 1.0
C A:LYS268 4.0 34.0 1.0
CA A:CYS269 4.0 34.8 1.0
O A:LEU267 4.1 34.8 1.0
O A:HOH481 4.6 50.8 1.0
CD A:LYS268 4.6 45.3 1.0
CB A:LYS268 4.8 38.6 1.0
N A:LYS268 4.9 35.3 1.0
C A:LEU267 4.9 34.4 1.0
N A:ASN270 4.9 35.0 1.0
CB A:LEU219 5.0 34.7 1.0

Chlorine binding site 5 out of 7 in 7vdp

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Chlorine binding site 5 out of 7 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl315

b:75.7
occ:1.00
 OH A:TYR236 3.2 46.0 1.0
O A:TYR239 3.4 38.6 1.0
N A:TYR239 3.5 38.5 1.0
SD A:MET241 4.0 48.3 1.0
CG2 A:THR221 4.1 38.1 1.0
CA A:PRO238 4.1 42.5 1.0
C A:TYR239 4.2 37.9 1.0
CZ A:TYR236 4.2 44.9 1.0
CA A:TYR239 4.3 37.7 1.0
CE A:MET230 4.3 49.2 1.0
C A:PRO238 4.3 40.1 1.0
CE1 A:TYR236 4.4 42.6 1.0
CB A:TYR239 4.5 37.5 1.0
O A:HOH414 4.7 59.4 1.0
CB A:PRO238 4.8 44.4 1.0
O A:LYS237 5.0 41.0 1.0

Chlorine binding site 6 out of 7 in 7vdp

Go back to Chlorine Binding Sites List in 7vdp
Chlorine binding site 6 out of 7 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Cl316

b:87.8
occ:1.00
 O A:GLY138 3.9 36.2 1.0
O A:HOH582 3.9 63.3 1.0
C A:GLY138 4.0 38.6 1.0
O A:ASN137 4.0 45.0 1.0
O A:HOH475 4.1 61.6 1.0
O A:HOH408 4.2 46.2 1.0
N A:GLU139 4.2 37.3 1.0
NE2 A:GLN109 4.3 35.6 1.0
CG A:GLU139 4.4 38.9 1.0
O A:HOH514 4.4 42.7 1.0
CA A:GLU139 4.4 36.1 1.0
OE1 A:GLN109 4.5 34.2 1.0
O A:HOH576 4.5 60.1 1.0
CD A:GLN109 4.5 33.1 1.0
CA A:GLY138 4.6 40.4 1.0
O A:HOH530 4.8 55.4 1.0
OG A:SER105 4.9 36.5 1.0
C A:ASN137 4.9 43.6 1.0

Chlorine binding site 7 out of 7 in 7vdp

Go back to Chlorine Binding Sites List in 7vdp
Chlorine binding site 7 out of 7 in the The Structure of Cyclin-Dependent Kinase 5 (CDK5) in Complex with P25 and Compound 1


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 1 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Cl404

b:73.2
occ:1.00
 O C:ARG165 3.4 36.2 1.0
O C:HOH515 3.5 36.1 1.0
N C:LYS167 3.8 41.5 1.0
CA C:LEU166 4.2 38.1 1.0
O C:HOH527 4.2 54.6 1.0
C C:ARG165 4.5 36.5 1.0
C C:LEU166 4.5 40.1 1.0
CB C:LYS167 4.6 47.2 1.0
CA C:LYS167 4.7 44.2 1.0
CG C:LYS167 4.7 49.9 1.0
CD2 C:LEU166 4.8 37.4 1.0
N C:LEU166 4.8 38.0 1.0
N C:HIS168 4.9 41.8 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: Sun Jul 13 08:02:57 2025

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