Fluorine in PDB 6by8: Menin in Complex with Mi-1482
Protein crystallography data
The structure of Menin in Complex with Mi-1482, PDB code: 6by8
was solved by
T.Borkin,
S.Klossowski,
J.Pollock,
B.Linhares,
T.Cierpicki,
J.Grembecka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
38.52 /
1.90
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.991,
80.222,
124.722,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.1 /
18.8
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Menin in Complex with Mi-1482
(pdb code 6by8). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the
Menin in Complex with Mi-1482, PDB code: 6by8:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 6by8
Go back to
Fluorine Binding Sites List in 6by8
Fluorine binding site 1 out
of 3 in the Menin in Complex with Mi-1482
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-1482 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:10.0
occ:1.00
|
FAD
|
A:FNV601
|
0.0
|
10.0
|
1.0
|
CBP
|
A:FNV601
|
1.3
|
12.1
|
1.0
|
FAE
|
A:FNV601
|
2.1
|
8.8
|
1.0
|
FAF
|
A:FNV601
|
2.1
|
10.3
|
1.0
|
CAT
|
A:FNV601
|
2.4
|
5.2
|
1.0
|
CBD
|
A:FNV601
|
2.9
|
5.4
|
1.0
|
O
|
A:HOH1007
|
2.9
|
23.2
|
1.0
|
CAK
|
A:FNV601
|
3.4
|
9.2
|
1.0
|
O
|
A:HOH1029
|
3.5
|
43.3
|
1.0
|
OG
|
A:SER155
|
3.6
|
9.2
|
1.0
|
O
|
A:HOH959
|
3.6
|
20.2
|
1.0
|
S
|
A:DMS602
|
3.7
|
21.8
|
0.9
|
CB
|
A:SER155
|
3.7
|
7.7
|
1.0
|
C2
|
A:DMS602
|
3.9
|
19.6
|
0.9
|
SBA
|
A:FNV601
|
3.9
|
8.7
|
1.0
|
O
|
A:DMS602
|
4.0
|
26.7
|
0.9
|
O
|
A:HOH857
|
4.1
|
16.1
|
1.0
|
C5
|
A:FNV601
|
4.4
|
9.7
|
1.0
|
CE1
|
A:PHE238
|
4.7
|
5.1
|
1.0
|
C4
|
A:FNV601
|
4.7
|
10.8
|
1.0
|
N
|
A:HIS181
|
4.7
|
6.2
|
1.0
|
C
|
A:ASP180
|
4.8
|
8.8
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 6by8
Go back to
Fluorine Binding Sites List in 6by8
Fluorine binding site 2 out
of 3 in the Menin in Complex with Mi-1482
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-1482 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:8.8
occ:1.00
|
FAE
|
A:FNV601
|
0.0
|
8.8
|
1.0
|
CBP
|
A:FNV601
|
1.3
|
12.1
|
1.0
|
FAF
|
A:FNV601
|
2.1
|
10.3
|
1.0
|
FAD
|
A:FNV601
|
2.1
|
10.0
|
1.0
|
CAT
|
A:FNV601
|
2.3
|
5.2
|
1.0
|
C
|
A:HIS181
|
3.0
|
6.0
|
1.0
|
N
|
A:HIS181
|
3.1
|
6.2
|
1.0
|
CA
|
A:HIS181
|
3.2
|
6.7
|
1.0
|
O
|
A:HIS181
|
3.2
|
7.8
|
1.0
|
O
|
A:HOH959
|
3.2
|
20.2
|
1.0
|
N
|
A:ALA182
|
3.5
|
5.5
|
1.0
|
O
|
A:HOH1007
|
3.5
|
23.2
|
1.0
|
CB
|
A:SER155
|
3.6
|
7.7
|
1.0
|
CBD
|
A:FNV601
|
3.6
|
5.4
|
1.0
|
C
|
A:ASP180
|
3.7
|
8.8
|
1.0
|
O
|
A:HOH742
|
3.8
|
24.7
|
1.0
|
CB
|
A:ALA182
|
3.9
|
5.5
|
1.0
|
O
|
A:ASP180
|
4.0
|
8.0
|
1.0
|
CA
|
A:ALA182
|
4.2
|
5.5
|
1.0
|
OG
|
A:SER155
|
4.3
|
9.2
|
1.0
|
CA
|
A:ASP180
|
4.5
|
8.2
|
1.0
|
CAK
|
A:FNV601
|
4.6
|
9.2
|
1.0
|
SBA
|
A:FNV601
|
4.6
|
8.7
|
1.0
|
O
|
A:HOH857
|
4.7
|
16.1
|
1.0
|
CB
|
A:HIS181
|
4.7
|
5.8
|
1.0
|
CA
|
A:SER155
|
4.8
|
7.8
|
1.0
|
O
|
A:SER178
|
4.9
|
7.5
|
1.0
|
N
|
A:ASP180
|
4.9
|
5.6
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 6by8
Go back to
Fluorine Binding Sites List in 6by8
Fluorine binding site 3 out
of 3 in the Menin in Complex with Mi-1482
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-1482 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:10.3
occ:1.00
|
FAF
|
A:FNV601
|
0.0
|
10.3
|
1.0
|
CBP
|
A:FNV601
|
1.3
|
12.1
|
1.0
|
FAE
|
A:FNV601
|
2.1
|
8.8
|
1.0
|
FAD
|
A:FNV601
|
2.1
|
10.0
|
1.0
|
CAT
|
A:FNV601
|
2.4
|
5.2
|
1.0
|
CBD
|
A:FNV601
|
2.9
|
5.4
|
1.0
|
SBA
|
A:FNV601
|
3.2
|
8.7
|
1.0
|
CB
|
A:SER155
|
3.3
|
7.7
|
1.0
|
CE1
|
A:PHE238
|
3.4
|
5.1
|
1.0
|
CD2
|
A:LEU177
|
3.6
|
5.9
|
1.0
|
OG
|
A:SER155
|
3.8
|
9.2
|
1.0
|
CB
|
A:ALA182
|
3.9
|
5.5
|
1.0
|
CZ
|
A:PHE238
|
4.0
|
9.5
|
1.0
|
O
|
A:HIS181
|
4.0
|
7.8
|
1.0
|
CAK
|
A:FNV601
|
4.0
|
9.2
|
1.0
|
C
|
A:HIS181
|
4.3
|
6.0
|
1.0
|
S
|
A:DMS602
|
4.3
|
21.8
|
0.9
|
CD1
|
A:PHE238
|
4.5
|
5.8
|
1.0
|
C4
|
A:FNV601
|
4.5
|
10.8
|
1.0
|
C2
|
A:DMS602
|
4.6
|
19.6
|
0.9
|
N
|
A:ALA182
|
4.6
|
5.5
|
1.0
|
CA
|
A:ALA182
|
4.7
|
5.5
|
1.0
|
CG
|
A:LEU177
|
4.7
|
7.8
|
1.0
|
CA
|
A:SER155
|
4.8
|
7.8
|
1.0
|
O
|
A:HOH1007
|
4.8
|
23.2
|
1.0
|
C5
|
A:FNV601
|
4.8
|
9.7
|
1.0
|
N
|
A:HIS181
|
4.8
|
6.2
|
1.0
|
O
|
A:HOH959
|
4.9
|
20.2
|
1.0
|
CA
|
A:HIS181
|
4.9
|
6.7
|
1.0
|
O
|
A:SER178
|
5.0
|
7.5
|
1.0
|
CB
|
A:LEU177
|
5.0
|
7.2
|
1.0
|
|
Reference:
D.Borkin,
S.Klossowski,
J.Pollock,
H.Miao,
B.M.Linhares,
K.Kempinska,
Z.Jin,
T.Purohit,
B.Wen,
M.He,
D.Sun,
T.Cierpicki,
J.Grembecka.
Complexity of Blocking Bivalent Protein-Protein Interactions: Development of A Highly Potent Inhibitor of the Menin-Mixed-Lineage Leukemia Interaction. J.Med.Chem. V. 61 4832 2018.
ISSN: ISSN 0022-2623
PubMed: 29738674
DOI: 10.1021/ACS.JMEDCHEM.8B00071
Page generated: Sun Dec 13 12:46:10 2020
|