Calcium in PDB 4a7b: MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22
Protein crystallography data
The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22, PDB code: 4a7b
was solved by
D.Hargreaves,
S.Gerhardt,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
72.02 /
2.20
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
135.854,
36.220,
95.568,
90.00,
131.10,
90.00
|
R / Rfree (%)
|
19.3 /
25.3
|
Other elements in 4a7b:
The structure of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 also contains other interesting chemical elements:
Calcium Binding Sites:
The binding sites of Calcium atom in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22
(pdb code 4a7b). This binding sites where shown within
5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the
MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22, PDB code: 4a7b:
Jump to Calcium binding site number:
1;
2;
3;
4;
Calcium binding site 1 out
of 4 in 4a7b
Go back to
Calcium Binding Sites List in 4a7b
Calcium binding site 1 out
of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 1 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1277
b:25.8
occ:1.00
|
O
|
A:HOH2048
|
2.3
|
20.5
|
1.0
|
O
|
A:GLY196
|
2.3
|
23.2
|
1.0
|
O
|
A:ASN194
|
2.4
|
31.2
|
1.0
|
O
|
A:ASP162
|
2.4
|
23.1
|
1.0
|
O
|
A:HOH2049
|
2.4
|
25.4
|
1.0
|
OD1
|
A:ASP198
|
2.5
|
22.2
|
1.0
|
CG
|
A:ASP198
|
3.4
|
21.8
|
1.0
|
C
|
A:GLY196
|
3.5
|
22.9
|
1.0
|
C
|
A:ASN194
|
3.5
|
28.9
|
1.0
|
C
|
A:ASP162
|
3.6
|
21.5
|
1.0
|
OD2
|
A:ASP198
|
3.9
|
22.4
|
1.0
|
N
|
A:GLY196
|
3.9
|
23.9
|
1.0
|
C
|
A:TYR195
|
4.0
|
24.5
|
1.0
|
N
|
A:ASP198
|
4.1
|
20.4
|
1.0
|
O
|
A:ALA161
|
4.1
|
24.8
|
1.0
|
O
|
A:HOH2072
|
4.1
|
34.0
|
1.0
|
O
|
A:TYR195
|
4.2
|
24.7
|
1.0
|
CA
|
A:GLY196
|
4.2
|
22.9
|
1.0
|
CA
|
A:ASP162
|
4.4
|
24.0
|
1.0
|
O
|
A:GLY192
|
4.4
|
25.5
|
1.0
|
N
|
A:TYR195
|
4.4
|
29.4
|
1.0
|
CA
|
A:ASN194
|
4.4
|
31.4
|
1.0
|
N
|
A:ASN194
|
4.4
|
31.5
|
1.0
|
CA
|
A:TYR195
|
4.5
|
28.2
|
1.0
|
O
|
A:HOH2050
|
4.5
|
29.9
|
1.0
|
N
|
A:GLY197
|
4.5
|
21.9
|
1.0
|
N
|
A:ILE163
|
4.6
|
21.3
|
1.0
|
CB
|
A:ASP198
|
4.6
|
19.7
|
1.0
|
C
|
A:GLY197
|
4.7
|
21.1
|
1.0
|
CA
|
A:GLY197
|
4.7
|
20.2
|
1.0
|
C
|
A:PRO193
|
4.7
|
29.7
|
1.0
|
CA
|
A:ASP198
|
4.8
|
20.6
|
1.0
|
CH2
|
A:TRP113
|
4.8
|
25.6
|
1.0
|
CA
|
A:ILE163
|
4.8
|
20.9
|
1.0
|
N
|
A:MET164
|
4.8
|
21.7
|
1.0
|
CG
|
A:MET164
|
4.8
|
21.0
|
1.0
|
O
|
A:PRO193
|
4.9
|
31.0
|
1.0
|
|
Calcium binding site 2 out
of 4 in 4a7b
Go back to
Calcium Binding Sites List in 4a7b
Calcium binding site 2 out
of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 2 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Ca1279
b:24.1
occ:1.00
|
O
|
A:GLY180
|
2.2
|
24.8
|
1.0
|
OE2
|
A:GLU205
|
2.3
|
28.6
|
1.0
|
OD2
|
A:ASP202
|
2.3
|
22.7
|
1.0
|
O
|
A:SER182
|
2.3
|
32.2
|
1.0
|
O
|
A:LEU184
|
2.4
|
24.3
|
1.0
|
OD1
|
A:ASP179
|
2.4
|
24.5
|
1.0
|
CG
|
A:ASP202
|
3.4
|
22.5
|
1.0
|
C
|
A:GLY180
|
3.4
|
25.6
|
1.0
|
CD
|
A:GLU205
|
3.5
|
25.8
|
1.0
|
C
|
A:SER182
|
3.5
|
31.3
|
1.0
|
C
|
A:LEU184
|
3.5
|
24.7
|
1.0
|
CG
|
A:ASP179
|
3.6
|
28.6
|
1.0
|
N
|
A:SER182
|
3.9
|
26.0
|
1.0
|
CB
|
A:ASP202
|
3.9
|
19.9
|
1.0
|
C
|
A:PRO181
|
4.0
|
25.7
|
1.0
|
N
|
A:LEU184
|
4.0
|
27.6
|
1.0
|
OD2
|
A:ASP179
|
4.1
|
31.5
|
1.0
|
N
|
A:GLY180
|
4.2
|
26.4
|
1.0
|
CA
|
A:SER182
|
4.2
|
29.4
|
1.0
|
OE1
|
A:GLU205
|
4.3
|
25.3
|
1.0
|
C
|
A:GLY183
|
4.3
|
31.8
|
1.0
|
N
|
A:ASP179
|
4.3
|
26.0
|
1.0
|
CA
|
A:LEU184
|
4.3
|
26.7
|
1.0
|
OD1
|
A:ASP202
|
4.3
|
19.3
|
1.0
|
O
|
A:PRO181
|
4.3
|
25.8
|
1.0
|
CA
|
A:PRO181
|
4.3
|
25.9
|
1.0
|
N
|
A:PRO181
|
4.3
|
26.1
|
1.0
|
CG
|
A:GLU205
|
4.4
|
24.3
|
1.0
|
C
|
A:ASP179
|
4.4
|
26.7
|
1.0
|
CA
|
A:GLY180
|
4.4
|
25.4
|
1.0
|
N
|
A:LEU185
|
4.4
|
22.0
|
1.0
|
N
|
A:GLY183
|
4.5
|
31.2
|
1.0
|
CA
|
A:GLY183
|
4.5
|
30.3
|
1.0
|
CA
|
A:LEU185
|
4.6
|
21.7
|
1.0
|
CA
|
A:ASP179
|
4.7
|
27.8
|
1.0
|
CB
|
A:ASP179
|
4.8
|
25.7
|
1.0
|
O
|
A:ASP179
|
4.8
|
29.8
|
1.0
|
CB
|
A:LEU184
|
4.9
|
27.3
|
1.0
|
O
|
A:GLY183
|
5.0
|
30.4
|
1.0
|
|
Calcium binding site 3 out
of 4 in 4a7b
Go back to
Calcium Binding Sites List in 4a7b
Calcium binding site 3 out
of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 3 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1275
b:22.5
occ:1.00
|
O
|
B:HOH2048
|
2.3
|
20.2
|
1.0
|
O
|
B:ASP162
|
2.3
|
20.4
|
1.0
|
O
|
B:ASN194
|
2.3
|
28.6
|
1.0
|
O
|
B:GLY196
|
2.4
|
23.7
|
1.0
|
OD1
|
B:ASP198
|
2.4
|
21.1
|
1.0
|
O
|
B:HOH2047
|
2.4
|
24.8
|
1.0
|
CG
|
B:ASP198
|
3.4
|
21.0
|
1.0
|
C
|
B:ASP162
|
3.4
|
21.8
|
1.0
|
C
|
B:GLY196
|
3.5
|
24.2
|
1.0
|
C
|
B:ASN194
|
3.6
|
29.9
|
1.0
|
OD2
|
B:ASP198
|
3.7
|
21.1
|
1.0
|
C
|
B:TYR195
|
3.9
|
27.7
|
1.0
|
N
|
B:GLY196
|
4.0
|
26.1
|
1.0
|
O
|
B:ALA161
|
4.1
|
23.7
|
1.0
|
O
|
B:TYR195
|
4.1
|
24.6
|
1.0
|
N
|
B:ASP198
|
4.2
|
20.9
|
1.0
|
CA
|
B:ASP162
|
4.2
|
21.8
|
1.0
|
CA
|
B:GLY196
|
4.3
|
25.3
|
1.0
|
O
|
B:HOH2060
|
4.3
|
42.8
|
1.0
|
O
|
B:HOH2061
|
4.3
|
28.0
|
1.0
|
CA
|
B:TYR195
|
4.4
|
30.1
|
1.0
|
N
|
B:TYR195
|
4.4
|
29.4
|
1.0
|
N
|
B:ASN194
|
4.4
|
32.3
|
1.0
|
N
|
B:ILE163
|
4.4
|
21.2
|
1.0
|
O
|
B:GLY192
|
4.4
|
26.2
|
1.0
|
N
|
B:GLY197
|
4.5
|
23.2
|
1.0
|
CA
|
B:ASN194
|
4.5
|
32.9
|
1.0
|
N
|
B:MET164
|
4.6
|
20.4
|
1.0
|
CB
|
B:ASP198
|
4.6
|
19.9
|
1.0
|
CA
|
B:GLY197
|
4.6
|
20.9
|
1.0
|
CA
|
B:ILE163
|
4.6
|
21.0
|
1.0
|
C
|
B:GLY197
|
4.7
|
21.1
|
1.0
|
C
|
B:PRO193
|
4.7
|
30.9
|
1.0
|
CG
|
B:MET164
|
4.8
|
19.2
|
1.0
|
CA
|
B:ASP198
|
4.8
|
20.2
|
1.0
|
O
|
B:PRO193
|
5.0
|
27.8
|
1.0
|
|
Calcium binding site 4 out
of 4 in 4a7b
Go back to
Calcium Binding Sites List in 4a7b
Calcium binding site 4 out
of 4 in the MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22
Mono view
Stereo pair view
|
A full contact list of Calcium with other atoms in the Ca binding
site number 4 of MMP13 in Complex with A Novel Selective Non Zinc Binding Inhibitor CMPD22 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Ca1276
b:30.7
occ:1.00
|
OE2
|
B:GLU205
|
2.2
|
27.1
|
1.0
|
O
|
B:LEU184
|
2.2
|
27.4
|
1.0
|
O
|
B:SER182
|
2.3
|
31.9
|
1.0
|
OD1
|
B:ASP179
|
2.3
|
31.8
|
1.0
|
O
|
B:GLY180
|
2.4
|
31.8
|
1.0
|
OD2
|
B:ASP202
|
2.5
|
28.7
|
1.0
|
C
|
B:LEU184
|
3.4
|
30.4
|
1.0
|
C
|
B:SER182
|
3.4
|
35.4
|
1.0
|
CD
|
B:GLU205
|
3.4
|
28.2
|
1.0
|
CG
|
B:ASP179
|
3.4
|
29.9
|
1.0
|
CG
|
B:ASP202
|
3.5
|
27.2
|
1.0
|
C
|
B:GLY180
|
3.7
|
32.2
|
1.0
|
N
|
B:SER182
|
3.8
|
35.3
|
1.0
|
N
|
B:LEU184
|
3.9
|
31.1
|
1.0
|
OD2
|
B:ASP179
|
3.9
|
32.3
|
1.0
|
CB
|
B:ASP202
|
4.0
|
26.0
|
1.0
|
C
|
B:PRO181
|
4.0
|
35.6
|
1.0
|
CA
|
B:SER182
|
4.1
|
35.8
|
1.0
|
CA
|
B:LEU184
|
4.1
|
31.1
|
1.0
|
N
|
B:GLY180
|
4.2
|
30.9
|
1.0
|
OE1
|
B:GLU205
|
4.2
|
30.6
|
1.0
|
C
|
B:GLY183
|
4.2
|
33.1
|
1.0
|
C
|
B:ASP179
|
4.3
|
31.6
|
1.0
|
N
|
B:ASP179
|
4.3
|
30.5
|
1.0
|
CG
|
B:GLU205
|
4.3
|
27.8
|
1.0
|
OD1
|
B:ASP202
|
4.4
|
27.4
|
1.0
|
O
|
B:PRO181
|
4.4
|
36.6
|
1.0
|
N
|
B:LEU185
|
4.4
|
27.8
|
1.0
|
N
|
B:GLY183
|
4.4
|
33.8
|
1.0
|
CA
|
B:PRO181
|
4.5
|
34.0
|
1.0
|
N
|
B:PRO181
|
4.6
|
32.3
|
1.0
|
CA
|
B:GLY180
|
4.6
|
30.4
|
1.0
|
CB
|
B:LEU184
|
4.6
|
31.8
|
1.0
|
CB
|
B:ASP179
|
4.6
|
30.8
|
1.0
|
CA
|
B:ASP179
|
4.6
|
31.6
|
1.0
|
CA
|
B:GLY183
|
4.6
|
32.6
|
1.0
|
CA
|
B:LEU185
|
4.6
|
27.8
|
1.0
|
O
|
B:ASP179
|
4.7
|
30.4
|
1.0
|
O
|
B:GLY183
|
4.8
|
31.3
|
1.0
|
|
Reference:
C.De Savi,
A.D.Morley,
I.Nash,
G.Karoutchi,
K.Page,
A.Ting,
S.Gerhardt.
Lead Optimisation of Selective Non-Zinc Binding Inhibitors of MMP13. Part 2. Bioorg.Med.Chem.Lett. V. 22 271 2012.
ISSN: ISSN 0960-894X
PubMed: 22153941
DOI: 10.1016/J.BMCL.2011.11.034
Page generated: Sat Jul 13 21:55:51 2024
|