Zinc in PDB 5tuz: Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
Enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
All present enzymatic activity of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124:
2.1.1.43;
Protein crystallography data
The structure of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124, PDB code: 5tuz
was solved by
N.Babault,
Y.Xiong,
J.Liu,
J.Jin,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
59.02 /
1.95
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
74.940,
95.780,
102.360,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
16.1 /
20.1
|
Zinc Binding Sites:
The binding sites of Zinc atom in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
(pdb code 5tuz). This binding sites where shown within
5.0 Angstroms radius around Zinc atom.
In total 8 binding sites of Zinc where determined in the
Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124, PDB code: 5tuz:
Jump to Zinc binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
Zinc binding site 1 out
of 8 in 5tuz
Go back to
Zinc Binding Sites List in 5tuz
Zinc binding site 1 out
of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 1 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn3002
b:16.1
occ:1.00
|
SG
|
A:CYS1105
|
2.3
|
15.1
|
1.0
|
SG
|
A:CYS1109
|
2.3
|
15.5
|
1.0
|
SG
|
A:CYS1075
|
2.3
|
15.8
|
1.0
|
SG
|
A:CYS1062
|
2.4
|
13.4
|
1.0
|
CB
|
A:CYS1105
|
3.2
|
14.2
|
1.0
|
CB
|
A:CYS1062
|
3.2
|
18.4
|
1.0
|
CB
|
A:CYS1109
|
3.3
|
11.8
|
1.0
|
CB
|
A:CYS1075
|
3.4
|
15.2
|
1.0
|
CA
|
A:CYS1105
|
3.6
|
12.1
|
1.0
|
N
|
A:CYS1062
|
3.6
|
13.5
|
1.0
|
ZN
|
A:ZN3003
|
3.8
|
14.6
|
1.0
|
ZN
|
A:ZN3004
|
3.8
|
15.2
|
1.0
|
CA
|
A:CYS1062
|
4.0
|
17.0
|
1.0
|
SG
|
A:CYS1111
|
4.2
|
13.6
|
1.0
|
SG
|
A:CYS1073
|
4.3
|
14.2
|
1.0
|
N
|
A:CYS1105
|
4.5
|
11.7
|
1.0
|
C
|
A:TYR1061
|
4.5
|
18.0
|
1.0
|
N
|
A:ASN1106
|
4.6
|
11.1
|
1.0
|
CA
|
A:CYS1109
|
4.6
|
17.1
|
1.0
|
C
|
A:CYS1105
|
4.6
|
14.1
|
1.0
|
CA
|
A:CYS1075
|
4.7
|
14.9
|
1.0
|
N
|
A:CYS1075
|
4.7
|
16.2
|
1.0
|
SG
|
A:CYS1068
|
4.7
|
14.1
|
1.0
|
CA
|
A:TYR1061
|
4.8
|
16.1
|
1.0
|
C
|
A:CYS1062
|
4.8
|
18.1
|
1.0
|
O
|
A:CYS1062
|
4.9
|
13.6
|
1.0
|
O
|
A:HOH3222
|
4.9
|
18.1
|
1.0
|
ND2
|
A:ASN1117
|
5.0
|
13.6
|
1.0
|
|
Zinc binding site 2 out
of 8 in 5tuz
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Zinc Binding Sites List in 5tuz
Zinc binding site 2 out
of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 2 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn3003
b:14.6
occ:1.00
|
SG
|
A:CYS1111
|
2.3
|
13.6
|
1.0
|
SG
|
A:CYS1115
|
2.3
|
14.9
|
1.0
|
SG
|
A:CYS1105
|
2.3
|
15.1
|
1.0
|
SG
|
A:CYS1068
|
2.4
|
14.1
|
1.0
|
CB
|
A:CYS1105
|
3.1
|
14.2
|
1.0
|
CB
|
A:CYS1111
|
3.2
|
11.4
|
1.0
|
CB
|
A:CYS1115
|
3.2
|
14.2
|
1.0
|
CB
|
A:CYS1068
|
3.3
|
15.6
|
1.0
|
ZN
|
A:ZN3004
|
3.7
|
15.2
|
1.0
|
ZN
|
A:ZN3002
|
3.8
|
16.1
|
1.0
|
SG
|
A:CYS1062
|
4.0
|
13.4
|
1.0
|
NH2
|
A:ARG1118
|
4.4
|
18.4
|
1.0
|
NE
|
A:ARG1118
|
4.4
|
15.8
|
1.0
|
CB
|
A:ASN1117
|
4.5
|
15.0
|
1.0
|
CA
|
A:CYS1105
|
4.6
|
12.1
|
1.0
|
CA
|
A:CYS1111
|
4.6
|
15.1
|
1.0
|
CA
|
A:CYS1115
|
4.7
|
16.4
|
1.0
|
CA
|
A:CYS1068
|
4.7
|
15.3
|
1.0
|
CZ
|
A:ARG1118
|
4.8
|
15.1
|
1.0
|
O
|
A:TRP1112
|
4.8
|
11.4
|
1.0
|
N
|
A:ASN1117
|
4.9
|
14.4
|
1.0
|
CB
|
A:CYS1109
|
5.0
|
11.8
|
1.0
|
|
Zinc binding site 3 out
of 8 in 5tuz
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Zinc Binding Sites List in 5tuz
Zinc binding site 3 out
of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 3 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn3004
b:15.2
occ:1.00
|
SG
|
A:CYS1068
|
2.3
|
14.1
|
1.0
|
SG
|
A:CYS1073
|
2.3
|
14.2
|
1.0
|
SG
|
A:CYS1062
|
2.3
|
13.4
|
1.0
|
SG
|
A:CYS1064
|
2.4
|
16.3
|
1.0
|
CB
|
A:CYS1062
|
3.2
|
18.4
|
1.0
|
CB
|
A:CYS1064
|
3.2
|
15.7
|
1.0
|
CB
|
A:CYS1068
|
3.3
|
15.6
|
1.0
|
CB
|
A:CYS1073
|
3.3
|
21.2
|
1.0
|
ZN
|
A:ZN3003
|
3.7
|
14.6
|
1.0
|
ZN
|
A:ZN3002
|
3.8
|
16.1
|
1.0
|
CA
|
A:CYS1073
|
3.9
|
15.3
|
1.0
|
CA
|
A:CYS1068
|
3.9
|
15.3
|
1.0
|
SG
|
A:CYS1105
|
4.0
|
15.1
|
1.0
|
N
|
A:CYS1064
|
4.4
|
15.5
|
1.0
|
CA
|
A:CYS1064
|
4.4
|
17.7
|
1.0
|
O
|
A:HOH3131
|
4.6
|
23.2
|
1.0
|
CA
|
A:CYS1062
|
4.6
|
17.0
|
1.0
|
C
|
A:CYS1073
|
4.7
|
17.1
|
1.0
|
N
|
A:MET1074
|
4.8
|
17.9
|
1.0
|
SG
|
A:CYS1111
|
4.8
|
13.6
|
1.0
|
N
|
A:CYS1068
|
4.8
|
15.7
|
1.0
|
O
|
A:HOH3217
|
4.8
|
20.0
|
1.0
|
O
|
A:HOH3170
|
4.8
|
35.8
|
1.0
|
CB
|
A:CYS1111
|
4.8
|
11.4
|
1.0
|
|
Zinc binding site 4 out
of 8 in 5tuz
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Zinc Binding Sites List in 5tuz
Zinc binding site 4 out
of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 4 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:Zn3005
b:20.2
occ:1.00
|
SG
|
A:CYS1256
|
2.3
|
19.8
|
1.0
|
SG
|
A:CYS1258
|
2.3
|
18.9
|
1.0
|
SG
|
A:CYS1203
|
2.3
|
21.0
|
1.0
|
SG
|
A:CYS1263
|
2.4
|
20.4
|
1.0
|
CB
|
A:CYS1263
|
3.3
|
19.7
|
1.0
|
CB
|
A:CYS1256
|
3.3
|
21.7
|
1.0
|
CB
|
A:CYS1258
|
3.3
|
17.7
|
1.0
|
CB
|
A:CYS1203
|
3.4
|
23.4
|
1.0
|
CA
|
A:CYS1263
|
3.8
|
25.4
|
1.0
|
O
|
A:HOH3188
|
3.9
|
21.2
|
1.0
|
N
|
A:CYS1203
|
4.1
|
18.1
|
1.0
|
N
|
A:CYS1258
|
4.1
|
20.9
|
1.0
|
N
|
A:ARG1264
|
4.2
|
22.0
|
1.0
|
NE2
|
A:HIS1201
|
4.2
|
21.5
|
1.0
|
CA
|
A:CYS1258
|
4.2
|
20.1
|
1.0
|
CD2
|
A:HIS1201
|
4.3
|
18.7
|
1.0
|
CA
|
A:CYS1203
|
4.3
|
19.6
|
1.0
|
C
|
A:CYS1263
|
4.5
|
20.1
|
1.0
|
N
|
A:HIS1265
|
4.6
|
21.9
|
1.0
|
CA
|
A:CYS1256
|
4.6
|
25.2
|
1.0
|
N
|
A:GLY1259
|
4.7
|
22.9
|
1.0
|
C
|
A:CYS1256
|
4.7
|
28.5
|
1.0
|
C
|
A:CYS1258
|
4.8
|
22.2
|
1.0
|
CB
|
A:HIS1265
|
5.0
|
26.0
|
1.0
|
O
|
A:CYS1256
|
5.0
|
26.6
|
1.0
|
|
Zinc binding site 5 out
of 8 in 5tuz
Go back to
Zinc Binding Sites List in 5tuz
Zinc binding site 5 out
of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 5 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn3002
b:17.1
occ:1.00
|
SG
|
B:CYS1075
|
2.3
|
15.7
|
1.0
|
SG
|
B:CYS1109
|
2.3
|
16.2
|
1.0
|
SG
|
B:CYS1105
|
2.4
|
15.4
|
1.0
|
SG
|
B:CYS1062
|
2.4
|
15.3
|
1.0
|
CB
|
B:CYS1105
|
3.2
|
14.8
|
1.0
|
CB
|
B:CYS1062
|
3.2
|
18.4
|
1.0
|
CB
|
B:CYS1109
|
3.3
|
16.9
|
1.0
|
CB
|
B:CYS1075
|
3.4
|
12.9
|
1.0
|
CA
|
B:CYS1105
|
3.6
|
13.3
|
1.0
|
N
|
B:CYS1062
|
3.6
|
17.2
|
1.0
|
ZN
|
B:ZN3004
|
3.8
|
17.6
|
1.0
|
ZN
|
B:ZN3003
|
3.8
|
15.7
|
1.0
|
CA
|
B:CYS1062
|
4.0
|
18.1
|
1.0
|
SG
|
B:CYS1111
|
4.1
|
16.4
|
1.0
|
SG
|
B:CYS1073
|
4.3
|
16.9
|
1.0
|
N
|
B:ASN1106
|
4.5
|
12.1
|
1.0
|
N
|
B:CYS1105
|
4.5
|
10.5
|
1.0
|
CA
|
B:CYS1109
|
4.6
|
16.0
|
1.0
|
C
|
B:TYR1061
|
4.6
|
20.4
|
1.0
|
C
|
B:CYS1105
|
4.6
|
14.5
|
1.0
|
SG
|
B:CYS1068
|
4.7
|
16.8
|
1.0
|
CA
|
B:CYS1075
|
4.7
|
14.6
|
1.0
|
N
|
B:CYS1075
|
4.7
|
15.4
|
1.0
|
C
|
B:CYS1062
|
4.8
|
19.0
|
1.0
|
CA
|
B:TYR1061
|
4.9
|
17.7
|
1.0
|
O
|
B:CYS1062
|
4.9
|
18.5
|
1.0
|
|
Zinc binding site 6 out
of 8 in 5tuz
Go back to
Zinc Binding Sites List in 5tuz
Zinc binding site 6 out
of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 6 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn3003
b:15.7
occ:1.00
|
SG
|
B:CYS1068
|
2.3
|
16.8
|
1.0
|
SG
|
B:CYS1115
|
2.3
|
15.0
|
1.0
|
SG
|
B:CYS1111
|
2.3
|
16.4
|
1.0
|
SG
|
B:CYS1105
|
2.4
|
15.4
|
1.0
|
CB
|
B:CYS1111
|
3.2
|
14.7
|
1.0
|
CB
|
B:CYS1105
|
3.2
|
14.8
|
1.0
|
CB
|
B:CYS1115
|
3.2
|
13.3
|
1.0
|
CB
|
B:CYS1068
|
3.3
|
13.4
|
1.0
|
ZN
|
B:ZN3004
|
3.7
|
17.6
|
1.0
|
ZN
|
B:ZN3002
|
3.8
|
17.1
|
1.0
|
SG
|
B:CYS1062
|
4.0
|
15.3
|
1.0
|
NE
|
B:ARG1118
|
4.3
|
13.4
|
1.0
|
NH2
|
B:ARG1118
|
4.4
|
17.4
|
1.0
|
CB
|
B:ASN1117
|
4.6
|
13.6
|
1.0
|
CA
|
B:CYS1111
|
4.6
|
15.7
|
1.0
|
CA
|
B:CYS1105
|
4.7
|
13.3
|
1.0
|
CA
|
B:CYS1068
|
4.7
|
15.8
|
1.0
|
CA
|
B:CYS1115
|
4.7
|
15.0
|
1.0
|
CZ
|
B:ARG1118
|
4.8
|
17.6
|
1.0
|
O
|
B:TRP1112
|
4.8
|
15.4
|
1.0
|
N
|
B:ASN1117
|
4.9
|
11.8
|
1.0
|
SG
|
B:CYS1073
|
5.0
|
16.9
|
1.0
|
|
Zinc binding site 7 out
of 8 in 5tuz
Go back to
Zinc Binding Sites List in 5tuz
Zinc binding site 7 out
of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 7 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn3004
b:17.6
occ:1.00
|
SG
|
B:CYS1068
|
2.3
|
16.8
|
1.0
|
SG
|
B:CYS1073
|
2.4
|
16.9
|
1.0
|
SG
|
B:CYS1062
|
2.4
|
15.3
|
1.0
|
SG
|
B:CYS1064
|
2.4
|
17.6
|
1.0
|
CB
|
B:CYS1062
|
3.1
|
18.4
|
1.0
|
CB
|
B:CYS1064
|
3.2
|
22.8
|
1.0
|
CB
|
B:CYS1073
|
3.2
|
15.5
|
1.0
|
CB
|
B:CYS1068
|
3.3
|
13.4
|
1.0
|
ZN
|
B:ZN3003
|
3.7
|
15.7
|
1.0
|
ZN
|
B:ZN3002
|
3.8
|
17.1
|
1.0
|
CA
|
B:CYS1068
|
3.9
|
15.8
|
1.0
|
CA
|
B:CYS1073
|
3.9
|
20.0
|
1.0
|
SG
|
B:CYS1105
|
4.0
|
15.4
|
1.0
|
N
|
B:CYS1064
|
4.4
|
20.5
|
1.0
|
CA
|
B:CYS1064
|
4.4
|
25.5
|
1.0
|
CA
|
B:CYS1062
|
4.6
|
18.1
|
1.0
|
O
|
B:HOH3141
|
4.6
|
22.2
|
1.0
|
C
|
B:CYS1073
|
4.7
|
22.1
|
1.0
|
SG
|
B:CYS1111
|
4.7
|
16.4
|
1.0
|
N
|
B:CYS1068
|
4.7
|
15.3
|
1.0
|
CB
|
B:CYS1111
|
4.8
|
14.7
|
1.0
|
O
|
B:HOH3134
|
4.8
|
20.5
|
1.0
|
N
|
B:MET1074
|
4.8
|
19.0
|
1.0
|
C
|
B:CYS1062
|
4.9
|
19.0
|
1.0
|
|
Zinc binding site 8 out
of 8 in 5tuz
Go back to
Zinc Binding Sites List in 5tuz
Zinc binding site 8 out
of 8 in the Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124
Mono view
Stereo pair view
|
A full contact list of Zinc with other atoms in the Zn binding
site number 8 of Structure of Human Glp Set-Domain (EHMT1) in Complex with Inhibitor MS0124 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:Zn3005
b:25.2
occ:1.00
|
SG
|
B:CYS1256
|
2.3
|
23.8
|
1.0
|
SG
|
B:CYS1258
|
2.3
|
23.8
|
1.0
|
SG
|
B:CYS1203
|
2.4
|
23.9
|
1.0
|
SG
|
B:CYS1263
|
2.4
|
27.8
|
1.0
|
CB
|
B:CYS1263
|
3.3
|
33.7
|
1.0
|
CB
|
B:CYS1258
|
3.3
|
21.6
|
1.0
|
CB
|
B:CYS1256
|
3.3
|
27.7
|
1.0
|
CB
|
B:CYS1203
|
3.6
|
22.2
|
1.0
|
CA
|
B:CYS1263
|
3.7
|
33.4
|
1.0
|
O
|
B:HOH3221
|
4.0
|
23.6
|
1.0
|
N
|
B:CYS1258
|
4.0
|
24.9
|
1.0
|
N
|
B:CYS1203
|
4.1
|
22.3
|
1.0
|
CA
|
B:CYS1258
|
4.2
|
24.6
|
1.0
|
N
|
B:ARG1264
|
4.2
|
33.8
|
1.0
|
NE2
|
B:HIS1201
|
4.3
|
20.5
|
1.0
|
CD2
|
B:HIS1201
|
4.4
|
20.7
|
1.0
|
C
|
B:CYS1263
|
4.4
|
33.0
|
1.0
|
CA
|
B:CYS1203
|
4.5
|
19.9
|
1.0
|
N
|
B:HIS1265
|
4.6
|
32.8
|
1.0
|
CA
|
B:CYS1256
|
4.6
|
32.9
|
1.0
|
C
|
B:CYS1256
|
4.7
|
30.8
|
1.0
|
N
|
B:GLY1259
|
4.8
|
26.6
|
1.0
|
O
|
B:CYS1256
|
4.8
|
31.0
|
1.0
|
C
|
B:CYS1258
|
4.9
|
30.3
|
1.0
|
N
|
B:CYS1263
|
5.0
|
32.3
|
1.0
|
CB
|
B:HIS1265
|
5.0
|
32.9
|
1.0
|
|
Reference:
Y.Xiong,
F.Li,
N.Babault,
A.Dong,
H.Zeng,
H.Wu,
X.Chen,
C.H.Arrowsmith,
P.J.Brown,
J.Liu,
M.Vedadi,
J.Jin.
Discovery of Potent and Selective Inhibitors For G9A-Like Protein (Glp) Lysine Methyltransferase. J. Med. Chem. V. 60 1876 2017.
ISSN: ISSN 1520-4804
PubMed: 28135087
DOI: 10.1021/ACS.JMEDCHEM.6B01645
Page generated: Mon Oct 28 08:48:18 2024
|