Fluorine in PDB 5db0: Menin in Complex with Mi-352
Protein crystallography data
The structure of Menin in Complex with Mi-352, PDB code: 5db0
was solved by
J.Pollock,
B.Dmitry,
T.Cierpicki,
J.Grembecka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
40.02 /
1.50
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.968,
79.970,
124.479,
90.00,
90.00,
90.00
|
|
R / Rfree (%)
|
16.1 /
18.5
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Menin in Complex with Mi-352
(pdb code 5db0). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the
Menin in Complex with Mi-352, PDB code: 5db0:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 5db0
Go back to
Fluorine Binding Sites List in 5db0
Fluorine binding site 1 out
of 6 in the Menin in Complex with Mi-352
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Menin in Complex with Mi-352 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F610
b:9.1
occ:0.50
|
FAE
|
A:58P610
|
0.0
|
9.1
|
0.5
|
|
FAE
|
A:6E6612
|
0.2
|
15.9
|
0.5
|
|
CBM
|
A:6E6612
|
1.3
|
14.6
|
0.5
|
|
CBM
|
A:58P610
|
1.3
|
8.4
|
0.5
|
|
FAF
|
A:6E6612
|
2.0
|
16.6
|
0.5
|
|
FAF
|
A:58P610
|
2.0
|
9.8
|
0.5
|
|
FAG
|
A:58P610
|
2.1
|
8.8
|
0.5
|
|
FAG
|
A:6E6612
|
2.2
|
15.0
|
0.5
|
|
CAU
|
A:58P610
|
2.3
|
8.0
|
0.5
|
|
CAU
|
A:6E6612
|
2.4
|
14.0
|
0.5
|
|
CBB
|
A:6E6612
|
2.9
|
13.3
|
0.5
|
|
CBB
|
A:58P610
|
2.9
|
7.6
|
0.5
|
|
SAZ
|
A:6E6612
|
3.2
|
14.2
|
0.5
|
|
SAZ
|
A:58P610
|
3.2
|
7.8
|
0.5
|
|
CB
|
A:SER155
|
3.3
|
10.9
|
1.0
|
|
CE1
|
A:PHE238
|
3.4
|
9.4
|
1.0
|
|
CD2
|
A:LEU177
|
3.6
|
10.0
|
1.0
|
|
OG
|
A:SER155
|
3.6
|
12.4
|
1.0
|
|
CB
|
A:ALA182
|
3.9
|
10.1
|
1.0
|
|
CAN
|
A:58P610
|
4.0
|
7.5
|
0.5
|
|
CAN
|
A:6E6612
|
4.0
|
13.4
|
0.5
|
|
CZ
|
A:PHE238
|
4.0
|
10.1
|
1.0
|
|
S
|
A:DMS609
|
4.1
|
15.1
|
0.5
|
|
O
|
A:HIS181
|
4.1
|
9.8
|
1.0
|
|
C
|
A:HIS181
|
4.4
|
9.6
|
1.0
|
|
C2
|
A:DMS609
|
4.5
|
16.0
|
0.5
|
|
C1
|
A:DMS613
|
4.5
|
37.9
|
0.5
|
|
CD1
|
A:PHE238
|
4.5
|
9.5
|
1.0
|
|
C4
|
A:6E6612
|
4.5
|
12.8
|
0.5
|
|
C4
|
A:58P610
|
4.5
|
7.1
|
0.5
|
|
N
|
A:ALA182
|
4.7
|
9.1
|
1.0
|
|
CA
|
A:SER155
|
4.7
|
10.7
|
1.0
|
|
CA
|
A:ALA182
|
4.8
|
9.1
|
1.0
|
|
C5
|
A:6E6612
|
4.8
|
12.4
|
0.5
|
|
C5
|
A:58P610
|
4.8
|
7.0
|
0.5
|
|
CG
|
A:LEU177
|
4.8
|
10.1
|
1.0
|
|
N
|
A:HIS181
|
5.0
|
9.6
|
1.0
|
|
O
|
A:DMS609
|
5.0
|
18.1
|
0.5
|
|
O
|
A:HOH1072
|
5.0
|
27.1
|
1.0
|
|
O
|
A:HOH1010
|
5.0
|
26.6
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 5db0
Go back to
Fluorine Binding Sites List in 5db0
Fluorine binding site 2 out
of 6 in the Menin in Complex with Mi-352
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Menin in Complex with Mi-352 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F610
b:9.8
occ:0.50
|
FAF
|
A:58P610
|
0.0
|
9.8
|
0.5
|
|
FAF
|
A:6E6612
|
0.1
|
16.6
|
0.5
|
|
CBM
|
A:58P610
|
1.3
|
8.4
|
0.5
|
|
CBM
|
A:6E6612
|
1.3
|
14.6
|
0.5
|
|
FAE
|
A:58P610
|
2.0
|
9.1
|
0.5
|
|
FAG
|
A:6E6612
|
2.1
|
15.0
|
0.5
|
|
FAG
|
A:58P610
|
2.1
|
8.8
|
0.5
|
|
FAE
|
A:6E6612
|
2.2
|
15.9
|
0.5
|
|
CAU
|
A:6E6612
|
2.4
|
14.0
|
0.5
|
|
CAU
|
A:58P610
|
2.4
|
8.0
|
0.5
|
|
CBB
|
A:6E6612
|
2.9
|
13.3
|
0.5
|
|
CBB
|
A:58P610
|
2.9
|
7.6
|
0.5
|
|
O
|
A:HOH1010
|
3.1
|
26.6
|
1.0
|
|
CAN
|
A:58P610
|
3.3
|
7.5
|
0.5
|
|
CAN
|
A:6E6612
|
3.3
|
13.4
|
0.5
|
|
OG
|
A:SER155
|
3.6
|
12.4
|
1.0
|
|
S
|
A:DMS609
|
3.7
|
15.1
|
0.5
|
|
O
|
A:HOH1072
|
3.7
|
27.1
|
1.0
|
|
CB
|
A:SER155
|
3.7
|
10.9
|
1.0
|
|
O
|
A:DMS609
|
3.9
|
18.1
|
0.5
|
|
SAZ
|
A:6E6612
|
3.9
|
14.2
|
0.5
|
|
SAZ
|
A:58P610
|
4.0
|
7.8
|
0.5
|
|
O
|
A:HOH914
|
4.0
|
18.7
|
1.0
|
|
C2
|
A:DMS609
|
4.0
|
16.0
|
0.5
|
|
C1
|
A:DMS613
|
4.2
|
37.9
|
0.5
|
|
C5
|
A:58P610
|
4.4
|
7.0
|
0.5
|
|
C5
|
A:6E6612
|
4.4
|
12.4
|
0.5
|
|
O
|
A:DMS613
|
4.4
|
40.8
|
0.5
|
|
N
|
A:HIS181
|
4.7
|
9.6
|
1.0
|
|
C4
|
A:58P610
|
4.7
|
7.1
|
0.5
|
|
C4
|
A:6E6612
|
4.7
|
12.8
|
0.5
|
|
C
|
A:ASP180
|
4.7
|
10.2
|
1.0
|
|
CE1
|
A:PHE238
|
4.8
|
9.4
|
1.0
|
|
S
|
A:DMS613
|
5.0
|
38.5
|
0.5
|
|
Fluorine binding site 3 out
of 6 in 5db0
Go back to
Fluorine Binding Sites List in 5db0
Fluorine binding site 3 out
of 6 in the Menin in Complex with Mi-352
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Menin in Complex with Mi-352 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F610
b:8.8
occ:0.50
|
FAG
|
A:58P610
|
0.0
|
8.8
|
0.5
|
|
FAG
|
A:6E6612
|
0.1
|
15.0
|
0.5
|
|
CBM
|
A:6E6612
|
1.3
|
14.6
|
0.5
|
|
CBM
|
A:58P610
|
1.3
|
8.4
|
0.5
|
|
FAE
|
A:6E6612
|
2.1
|
15.9
|
0.5
|
|
FAF
|
A:58P610
|
2.1
|
9.8
|
0.5
|
|
FAF
|
A:6E6612
|
2.1
|
16.6
|
0.5
|
|
FAE
|
A:58P610
|
2.1
|
9.1
|
0.5
|
|
CAU
|
A:6E6612
|
2.4
|
14.0
|
0.5
|
|
CAU
|
A:58P610
|
2.4
|
8.0
|
0.5
|
|
C
|
A:HIS181
|
3.0
|
9.6
|
1.0
|
|
CA
|
A:HIS181
|
3.1
|
9.2
|
1.0
|
|
N
|
A:HIS181
|
3.2
|
9.6
|
1.0
|
|
O
|
A:HIS181
|
3.2
|
9.8
|
1.0
|
|
O
|
A:HOH1072
|
3.3
|
27.1
|
1.0
|
|
N
|
A:ALA182
|
3.4
|
9.1
|
1.0
|
|
CB
|
A:SER155
|
3.6
|
10.9
|
1.0
|
|
C
|
A:ASP180
|
3.6
|
10.2
|
1.0
|
|
CBB
|
A:6E6612
|
3.7
|
13.3
|
0.5
|
|
CBB
|
A:58P610
|
3.7
|
7.6
|
0.5
|
|
O
|
A:HOH746
|
3.8
|
23.8
|
1.0
|
|
CB
|
A:ALA182
|
3.8
|
10.1
|
1.0
|
|
O
|
A:HOH1010
|
3.9
|
26.6
|
1.0
|
|
O
|
A:ASP180
|
4.0
|
11.3
|
1.0
|
|
CA
|
A:ALA182
|
4.2
|
9.1
|
1.0
|
|
OG
|
A:SER155
|
4.2
|
12.4
|
1.0
|
|
CA
|
A:ASP180
|
4.5
|
10.0
|
1.0
|
|
CAN
|
A:58P610
|
4.6
|
7.5
|
0.5
|
|
CAN
|
A:6E6612
|
4.6
|
13.4
|
0.5
|
|
O
|
A:HOH914
|
4.6
|
18.7
|
1.0
|
|
CB
|
A:HIS181
|
4.7
|
10.2
|
1.0
|
|
SAZ
|
A:6E6612
|
4.7
|
14.2
|
0.5
|
|
SAZ
|
A:58P610
|
4.7
|
7.8
|
0.5
|
|
CA
|
A:SER155
|
4.7
|
10.7
|
1.0
|
|
CD2
|
A:LEU177
|
4.9
|
10.0
|
1.0
|
|
N
|
A:ASP180
|
5.0
|
9.6
|
1.0
|
|
O
|
A:SER178
|
5.0
|
9.8
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 5db0
Go back to
Fluorine Binding Sites List in 5db0
Fluorine binding site 4 out
of 6 in the Menin in Complex with Mi-352
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Menin in Complex with Mi-352 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F612
b:15.9
occ:0.50
|
FAE
|
A:6E6612
|
0.0
|
15.9
|
0.5
|
|
FAE
|
A:58P610
|
0.2
|
9.1
|
0.5
|
|
CBM
|
A:6E6612
|
1.3
|
14.6
|
0.5
|
|
CBM
|
A:58P610
|
1.3
|
8.4
|
0.5
|
|
FAG
|
A:58P610
|
2.1
|
8.8
|
0.5
|
|
FAF
|
A:6E6612
|
2.1
|
16.6
|
0.5
|
|
FAG
|
A:6E6612
|
2.2
|
15.0
|
0.5
|
|
FAF
|
A:58P610
|
2.2
|
9.8
|
0.5
|
|
CAU
|
A:58P610
|
2.3
|
8.0
|
0.5
|
|
CAU
|
A:6E6612
|
2.3
|
14.0
|
0.5
|
|
CBB
|
A:6E6612
|
2.9
|
13.3
|
0.5
|
|
CBB
|
A:58P610
|
2.9
|
7.6
|
0.5
|
|
SAZ
|
A:6E6612
|
3.2
|
14.2
|
0.5
|
|
SAZ
|
A:58P610
|
3.2
|
7.8
|
0.5
|
|
CB
|
A:SER155
|
3.3
|
10.9
|
1.0
|
|
CD2
|
A:LEU177
|
3.4
|
10.0
|
1.0
|
|
CE1
|
A:PHE238
|
3.5
|
9.4
|
1.0
|
|
OG
|
A:SER155
|
3.7
|
12.4
|
1.0
|
|
CB
|
A:ALA182
|
3.8
|
10.1
|
1.0
|
|
O
|
A:HIS181
|
3.9
|
9.8
|
1.0
|
|
CAN
|
A:58P610
|
4.0
|
7.5
|
0.5
|
|
CAN
|
A:6E6612
|
4.0
|
13.4
|
0.5
|
|
CZ
|
A:PHE238
|
4.1
|
10.1
|
1.0
|
|
C
|
A:HIS181
|
4.2
|
9.6
|
1.0
|
|
S
|
A:DMS609
|
4.3
|
15.1
|
0.5
|
|
N
|
A:ALA182
|
4.5
|
9.1
|
1.0
|
|
CD1
|
A:PHE238
|
4.5
|
9.5
|
1.0
|
|
C4
|
A:6E6612
|
4.6
|
12.8
|
0.5
|
|
C4
|
A:58P610
|
4.6
|
7.1
|
0.5
|
|
CA
|
A:ALA182
|
4.6
|
9.1
|
1.0
|
|
C2
|
A:DMS609
|
4.7
|
16.0
|
0.5
|
|
CG
|
A:LEU177
|
4.7
|
10.1
|
1.0
|
|
C1
|
A:DMS613
|
4.7
|
37.9
|
0.5
|
|
CA
|
A:SER155
|
4.7
|
10.7
|
1.0
|
|
N
|
A:HIS181
|
4.8
|
9.6
|
1.0
|
|
C5
|
A:6E6612
|
4.9
|
12.4
|
0.5
|
|
C5
|
A:58P610
|
4.9
|
7.0
|
0.5
|
|
CA
|
A:HIS181
|
4.9
|
9.2
|
1.0
|
|
CB
|
A:LEU177
|
5.0
|
9.2
|
1.0
|
|
O
|
A:SER178
|
5.0
|
9.8
|
1.0
|
|
Fluorine binding site 5 out
of 6 in 5db0
Go back to
Fluorine Binding Sites List in 5db0
Fluorine binding site 5 out
of 6 in the Menin in Complex with Mi-352
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Menin in Complex with Mi-352 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F612
b:16.6
occ:0.50
|
FAF
|
A:6E6612
|
0.0
|
16.6
|
0.5
|
|
FAF
|
A:58P610
|
0.1
|
9.8
|
0.5
|
|
CBM
|
A:58P610
|
1.3
|
8.4
|
0.5
|
|
CBM
|
A:6E6612
|
1.3
|
14.6
|
0.5
|
|
FAE
|
A:58P610
|
2.0
|
9.1
|
0.5
|
|
FAE
|
A:6E6612
|
2.1
|
15.9
|
0.5
|
|
FAG
|
A:6E6612
|
2.1
|
15.0
|
0.5
|
|
FAG
|
A:58P610
|
2.1
|
8.8
|
0.5
|
|
CAU
|
A:6E6612
|
2.4
|
14.0
|
0.5
|
|
CAU
|
A:58P610
|
2.4
|
8.0
|
0.5
|
|
CBB
|
A:6E6612
|
2.8
|
13.3
|
0.5
|
|
CBB
|
A:58P610
|
2.9
|
7.6
|
0.5
|
|
O
|
A:HOH1010
|
3.2
|
26.6
|
1.0
|
|
CAN
|
A:58P610
|
3.3
|
7.5
|
0.5
|
|
CAN
|
A:6E6612
|
3.3
|
13.4
|
0.5
|
|
OG
|
A:SER155
|
3.5
|
12.4
|
1.0
|
|
S
|
A:DMS609
|
3.6
|
15.1
|
0.5
|
|
CB
|
A:SER155
|
3.7
|
10.9
|
1.0
|
|
O
|
A:HOH1072
|
3.8
|
27.1
|
1.0
|
|
SAZ
|
A:6E6612
|
3.9
|
14.2
|
0.5
|
|
O
|
A:DMS609
|
3.9
|
18.1
|
0.5
|
|
SAZ
|
A:58P610
|
3.9
|
7.8
|
0.5
|
|
C2
|
A:DMS609
|
4.0
|
16.0
|
0.5
|
|
O
|
A:HOH914
|
4.0
|
18.7
|
1.0
|
|
C1
|
A:DMS613
|
4.1
|
37.9
|
0.5
|
|
C5
|
A:58P610
|
4.4
|
7.0
|
0.5
|
|
C5
|
A:6E6612
|
4.4
|
12.4
|
0.5
|
|
O
|
A:DMS613
|
4.4
|
40.8
|
0.5
|
|
C4
|
A:58P610
|
4.6
|
7.1
|
0.5
|
|
C4
|
A:6E6612
|
4.6
|
12.8
|
0.5
|
|
CE1
|
A:PHE238
|
4.7
|
9.4
|
1.0
|
|
N
|
A:HIS181
|
4.7
|
9.6
|
1.0
|
|
C
|
A:ASP180
|
4.8
|
10.2
|
1.0
|
|
S
|
A:DMS613
|
4.9
|
38.5
|
0.5
|
|
Fluorine binding site 6 out
of 6 in 5db0
Go back to
Fluorine Binding Sites List in 5db0
Fluorine binding site 6 out
of 6 in the Menin in Complex with Mi-352
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Menin in Complex with Mi-352 within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F612
b:15.0
occ:0.50
|
FAG
|
A:6E6612
|
0.0
|
15.0
|
0.5
|
|
FAG
|
A:58P610
|
0.1
|
8.8
|
0.5
|
|
CBM
|
A:6E6612
|
1.3
|
14.6
|
0.5
|
|
CBM
|
A:58P610
|
1.3
|
8.4
|
0.5
|
|
FAF
|
A:58P610
|
2.1
|
9.8
|
0.5
|
|
FAF
|
A:6E6612
|
2.1
|
16.6
|
0.5
|
|
FAE
|
A:6E6612
|
2.2
|
15.9
|
0.5
|
|
FAE
|
A:58P610
|
2.2
|
9.1
|
0.5
|
|
CAU
|
A:6E6612
|
2.3
|
14.0
|
0.5
|
|
CAU
|
A:58P610
|
2.4
|
8.0
|
0.5
|
|
C
|
A:HIS181
|
3.0
|
9.6
|
1.0
|
|
CA
|
A:HIS181
|
3.1
|
9.2
|
1.0
|
|
N
|
A:HIS181
|
3.1
|
9.6
|
1.0
|
|
O
|
A:HIS181
|
3.2
|
9.8
|
1.0
|
|
O
|
A:HOH1072
|
3.2
|
27.1
|
1.0
|
|
N
|
A:ALA182
|
3.5
|
9.1
|
1.0
|
|
C
|
A:ASP180
|
3.6
|
10.2
|
1.0
|
|
CBB
|
A:6E6612
|
3.7
|
13.3
|
0.5
|
|
CBB
|
A:58P610
|
3.7
|
7.6
|
0.5
|
|
CB
|
A:SER155
|
3.7
|
10.9
|
1.0
|
|
O
|
A:HOH746
|
3.8
|
23.8
|
1.0
|
|
O
|
A:HOH1010
|
3.8
|
26.6
|
1.0
|
|
O
|
A:ASP180
|
3.9
|
11.3
|
1.0
|
|
CB
|
A:ALA182
|
3.9
|
10.1
|
1.0
|
|
CA
|
A:ALA182
|
4.2
|
9.1
|
1.0
|
|
OG
|
A:SER155
|
4.3
|
12.4
|
1.0
|
|
CA
|
A:ASP180
|
4.4
|
10.0
|
1.0
|
|
CAN
|
A:58P610
|
4.5
|
7.5
|
0.5
|
|
CAN
|
A:6E6612
|
4.6
|
13.4
|
0.5
|
|
CB
|
A:HIS181
|
4.6
|
10.2
|
1.0
|
|
O
|
A:HOH914
|
4.6
|
18.7
|
1.0
|
|
SAZ
|
A:6E6612
|
4.7
|
14.2
|
0.5
|
|
SAZ
|
A:58P610
|
4.7
|
7.8
|
0.5
|
|
CA
|
A:SER155
|
4.8
|
10.7
|
1.0
|
|
N
|
A:ASP180
|
4.9
|
9.6
|
1.0
|
|
O
|
A:SER178
|
5.0
|
9.8
|
1.0
|
|
CD2
|
A:LEU177
|
5.0
|
10.0
|
1.0
|
|
Reference:
D.Borkin,
J.Pollock,
K.Kempinska,
T.Purohit,
X.Li,
B.Wen,
T.Zhao,
H.Miao,
S.Shukla,
M.He,
D.Sun,
T.Cierpicki,
J.Grembecka.
Property Focused Structure-Based Optimization of Small Molecule Inhibitors of the Protein-Protein Interaction Between Menin and Mixed Lineage Leukemia (Mll). J.Med.Chem. V. 59 892 2016.
ISSN: ISSN 0022-2623
PubMed: 26744767
DOI: 10.1021/ACS.JMEDCHEM.5B01305
Page generated: Tue Jul 15 02:58:08 2025
|
