Chlorine in PDB 2xnn: Structure of NEK2 Bound to CCT242430
Enzymatic activity of Structure of NEK2 Bound to CCT242430
All present enzymatic activity of Structure of NEK2 Bound to CCT242430:
2.7.11.1;
Protein crystallography data
The structure of Structure of NEK2 Bound to CCT242430, PDB code: 2xnn
was solved by
C.Mas-Droux,
R.Bayliss,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
31.243 /
2.50
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
101.210,
56.850,
80.400,
90.00,
133.21,
90.00
|
R / Rfree (%)
|
17.18 /
23.74
|
Other elements in 2xnn:
The structure of Structure of NEK2 Bound to CCT242430 also contains other interesting chemical elements:
Chlorine Binding Sites:
The binding sites of Chlorine atom in the Structure of NEK2 Bound to CCT242430
(pdb code 2xnn). This binding sites where shown within
5.0 Angstroms radius around Chlorine atom.
In total 5 binding sites of Chlorine where determined in the
Structure of NEK2 Bound to CCT242430, PDB code: 2xnn:
Jump to Chlorine binding site number:
1;
2;
3;
4;
5;
Chlorine binding site 1 out
of 5 in 2xnn
Go back to
Chlorine Binding Sites List in 2xnn
Chlorine binding site 1 out
of 5 in the Structure of NEK2 Bound to CCT242430
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 1 of Structure of NEK2 Bound to CCT242430 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1281
b:51.5
occ:1.00
|
O
|
A:ARG235
|
3.4
|
20.7
|
1.0
|
NH2
|
A:ARG234
|
3.7
|
16.1
|
1.0
|
NE
|
A:ARG234
|
3.9
|
17.9
|
1.0
|
O2
|
A:EDO1290
|
4.2
|
28.6
|
1.0
|
CZ
|
A:ARG234
|
4.2
|
27.1
|
1.0
|
CE1
|
A:TYR238
|
4.4
|
14.0
|
1.0
|
CA
|
A:PRO237
|
4.5
|
10.8
|
1.0
|
C
|
A:ARG235
|
4.5
|
17.9
|
1.0
|
O
|
A:HOH2064
|
4.6
|
21.4
|
1.0
|
O
|
A:ILE236
|
4.6
|
12.0
|
1.0
|
N
|
A:PRO237
|
4.7
|
10.5
|
1.0
|
C
|
A:ILE236
|
4.7
|
14.4
|
1.0
|
CD1
|
A:TYR238
|
4.8
|
10.7
|
1.0
|
CB
|
A:ARG234
|
4.8
|
11.1
|
1.0
|
|
Chlorine binding site 2 out
of 5 in 2xnn
Go back to
Chlorine Binding Sites List in 2xnn
Chlorine binding site 2 out
of 5 in the Structure of NEK2 Bound to CCT242430
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 2 of Structure of NEK2 Bound to CCT242430 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1282
b:66.7
occ:1.00
|
C
|
A:ARG105
|
3.6
|
51.6
|
1.0
|
O
|
A:ARG105
|
3.6
|
53.9
|
1.0
|
CA
|
A:ARG105
|
3.8
|
56.2
|
1.0
|
CZ
|
A:TYR107
|
4.0
|
32.1
|
1.0
|
CB
|
A:ARG105
|
4.1
|
62.0
|
1.0
|
N
|
A:GLN106
|
4.1
|
43.3
|
1.0
|
CE2
|
A:TYR107
|
4.1
|
23.8
|
1.0
|
CE1
|
A:TYR107
|
4.2
|
22.1
|
1.0
|
OH
|
A:TYR107
|
4.2
|
35.2
|
1.0
|
CD1
|
A:LEU212
|
4.4
|
23.2
|
1.0
|
CD2
|
A:TYR107
|
4.6
|
33.4
|
1.0
|
CD1
|
A:TYR107
|
4.6
|
32.1
|
1.0
|
O
|
A:GLY101
|
4.7
|
29.6
|
1.0
|
CG
|
A:TYR107
|
4.8
|
30.1
|
1.0
|
CA
|
A:GLN106
|
4.8
|
37.6
|
0.9
|
C
|
A:GLN106
|
5.0
|
35.6
|
1.0
|
N
|
A:TYR107
|
5.0
|
27.2
|
1.0
|
|
Chlorine binding site 3 out
of 5 in 2xnn
Go back to
Chlorine Binding Sites List in 2xnn
Chlorine binding site 3 out
of 5 in the Structure of NEK2 Bound to CCT242430
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 3 of Structure of NEK2 Bound to CCT242430 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1283
b:55.0
occ:1.00
|
ND1
|
A:HIS277
|
2.9
|
32.1
|
1.0
|
O
|
A:HOH2057
|
2.9
|
35.2
|
1.0
|
ND2
|
A:ASN154
|
3.4
|
13.3
|
1.0
|
CB
|
A:HIS277
|
3.5
|
19.7
|
1.0
|
CG
|
A:HIS277
|
3.5
|
32.5
|
1.0
|
CB
|
A:PRO65
|
3.6
|
15.6
|
1.0
|
CG
|
A:ASN154
|
3.7
|
23.7
|
1.0
|
O
|
A:PRO65
|
3.9
|
16.7
|
1.0
|
CE1
|
A:HIS277
|
3.9
|
33.3
|
1.0
|
OD1
|
A:ASN154
|
4.1
|
19.2
|
1.0
|
O
|
A:HIS278
|
4.2
|
16.1
|
1.0
|
N
|
A:HIS278
|
4.2
|
16.7
|
1.0
|
CE1
|
A:HIS279
|
4.2
|
38.0
|
1.0
|
ND1
|
A:HIS279
|
4.2
|
31.3
|
1.0
|
CB
|
A:ASN154
|
4.2
|
20.7
|
1.0
|
C
|
A:HIS278
|
4.3
|
24.7
|
1.0
|
CA
|
A:PRO65
|
4.3
|
17.6
|
1.0
|
NZ
|
A:LYS156
|
4.3
|
18.4
|
1.0
|
CA
|
A:HIS277
|
4.4
|
18.9
|
1.0
|
C
|
A:PRO65
|
4.4
|
18.4
|
1.0
|
C
|
A:HIS277
|
4.5
|
21.1
|
1.0
|
N
|
A:HIS279
|
4.6
|
30.0
|
1.0
|
CE
|
A:LYS156
|
4.6
|
21.1
|
1.0
|
CD2
|
A:HIS277
|
4.7
|
36.5
|
1.0
|
NE2
|
A:HIS279
|
4.7
|
46.5
|
1.0
|
CA
|
A:HIS278
|
4.8
|
22.6
|
1.0
|
CG
|
A:HIS279
|
4.8
|
40.4
|
1.0
|
CA
|
A:HIS279
|
4.9
|
34.4
|
1.0
|
OD2
|
A:ASP150
|
4.9
|
26.8
|
1.0
|
NE2
|
A:HIS277
|
4.9
|
29.9
|
1.0
|
CG
|
A:PRO65
|
4.9
|
23.7
|
1.0
|
|
Chlorine binding site 4 out
of 5 in 2xnn
Go back to
Chlorine Binding Sites List in 2xnn
Chlorine binding site 4 out
of 5 in the Structure of NEK2 Bound to CCT242430
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 4 of Structure of NEK2 Bound to CCT242430 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1284
b:52.5
occ:1.00
|
N
|
A:VAL262
|
3.2
|
20.6
|
1.0
|
CA
|
A:SER261
|
3.6
|
20.9
|
1.0
|
CB
|
A:SER261
|
3.6
|
15.1
|
1.0
|
CG2
|
A:VAL262
|
3.7
|
19.0
|
1.0
|
C
|
A:SER261
|
3.9
|
19.8
|
1.0
|
CB
|
A:VAL262
|
4.0
|
21.9
|
1.0
|
CA
|
A:VAL262
|
4.1
|
19.0
|
1.0
|
CD1
|
A:ILE199
|
4.5
|
15.7
|
1.0
|
CB
|
A:GLU195
|
4.5
|
31.2
|
1.0
|
CG1
|
A:ILE199
|
4.6
|
14.2
|
1.0
|
OE2
|
A:GLU263
|
4.6
|
21.0
|
1.0
|
CE
|
A:LYS196
|
4.6
|
13.6
|
1.0
|
ND1
|
A:HIS128
|
4.7
|
36.4
|
1.0
|
CE1
|
A:HIS128
|
4.7
|
41.5
|
1.0
|
OG
|
A:SER261
|
4.8
|
17.9
|
1.0
|
OE1
|
A:GLU195
|
4.8
|
44.5
|
1.0
|
O
|
A:GLU195
|
4.9
|
31.8
|
1.0
|
CD
|
A:LYS196
|
4.9
|
15.6
|
1.0
|
N
|
A:SER261
|
4.9
|
25.6
|
1.0
|
|
Chlorine binding site 5 out
of 5 in 2xnn
Go back to
Chlorine Binding Sites List in 2xnn
Chlorine binding site 5 out
of 5 in the Structure of NEK2 Bound to CCT242430
 Mono view
 Stereo pair view
|
A full contact list of Chlorine with other atoms in the Cl binding
site number 5 of Structure of NEK2 Bound to CCT242430 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Cl1291
b:65.2
occ:1.00
|
O
|
A:GLU230
|
4.0
|
37.4
|
1.0
|
NZ
|
A:LYS232
|
4.0
|
27.4
|
0.3
|
O
|
A:GLY231
|
4.2
|
31.5
|
1.0
|
CG
|
A:LYS232
|
4.3
|
26.6
|
0.3
|
O
|
A:HOH2091
|
4.4
|
30.0
|
1.0
|
CG
|
A:LYS232
|
4.6
|
27.1
|
0.7
|
C
|
A:GLY231
|
4.6
|
30.2
|
1.0
|
CE
|
A:LYS232
|
4.7
|
24.0
|
0.3
|
O
|
A:HOH2073
|
4.7
|
27.8
|
1.0
|
|
Reference:
S.Solanki,
P.Innocenti,
C.Mas-Droux,
K.Boxall,
C.Barillari,
R.L.Van Montfort,
G.W.Aherne,
R.Bayliss,
S.Hoelder.
Benzimidazole Inhibitors Induce A Dfg-Out Conformation of Never in Mitosis Gene A-Related Kinase 2 (NEK2) Without Binding to the Back Pocket and Reveal A Nonlinear Structure-Activity Relationship. J.Med.Chem. V. 54 1626 2011.
ISSN: ISSN 0022-2623
PubMed: 21366329
DOI: 10.1021/JM1011726
Page generated: Sat Jul 20 14:02:28 2024
|