Fluorine in PDB 8va6: Menin in Complex with Ziftomenib (Ko-539)
Protein crystallography data
The structure of Menin in Complex with Ziftomenib (Ko-539), PDB code: 8va6
was solved by
B.D.Clegg,
B.M.Linhares,
T.Cierpicki,
J.Grembecka,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
41.47 /
1.57
|
|
Space group
|
P 21 21 21
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
48.395,
80.181,
124.924,
90,
90,
90
|
|
R / Rfree (%)
|
15.8 /
19.3
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Menin in Complex with Ziftomenib (Ko-539)
(pdb code 8va6). 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 Ziftomenib (Ko-539), PDB code: 8va6:
Jump to Fluorine binding site number:
1;
2;
3;
Fluorine binding site 1 out
of 3 in 8va6
Go back to
Fluorine Binding Sites List in 8va6
Fluorine binding site 1 out
of 3 in the Menin in Complex with Ziftomenib (Ko-539)
 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 Ziftomenib (Ko-539) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:16.8
occ:1.00
|
F1
|
A:K5O601
|
0.0
|
16.8
|
1.0
|
|
C32
|
A:K5O601
|
1.3
|
18.8
|
1.0
|
|
F2
|
A:K5O601
|
2.1
|
20.1
|
1.0
|
|
F3
|
A:K5O601
|
2.1
|
18.5
|
1.0
|
|
C31
|
A:K5O601
|
2.4
|
15.3
|
1.0
|
|
H44
|
A:K5O601
|
2.6
|
15.3
|
1.0
|
|
H43
|
A:K5O601
|
2.6
|
15.3
|
1.0
|
|
HB3
|
A:SER155
|
2.8
|
17.0
|
1.0
|
|
HA
|
A:HIS181
|
2.9
|
15.1
|
1.0
|
|
C
|
A:HIS181
|
3.0
|
14.9
|
1.0
|
|
HB1
|
A:ALA182
|
3.0
|
15.7
|
1.0
|
|
O
|
A:HIS181
|
3.2
|
14.0
|
1.0
|
|
CA
|
A:HIS181
|
3.2
|
15.1
|
1.0
|
|
N
|
A:HIS181
|
3.2
|
14.4
|
1.0
|
|
H
|
A:HIS181
|
3.4
|
14.6
|
1.0
|
|
N
|
A:ALA182
|
3.4
|
13.8
|
1.0
|
|
O
|
A:HOH960
|
3.5
|
38.0
|
1.0
|
|
CB
|
A:SER155
|
3.6
|
17.2
|
1.0
|
|
C30
|
A:K5O601
|
3.7
|
12.8
|
1.0
|
|
HB2
|
A:SER155
|
3.7
|
17.0
|
1.0
|
|
C
|
A:ASP180
|
3.7
|
14.7
|
1.0
|
|
CB
|
A:ALA182
|
3.7
|
16.0
|
1.0
|
|
H
|
A:ALA182
|
3.8
|
14.4
|
1.0
|
|
HB2
|
A:ALA182
|
3.9
|
15.7
|
1.0
|
|
HG
|
A:SER155
|
4.0
|
17.7
|
0.0
|
|
HD22
|
A:LEU177
|
4.1
|
15.6
|
1.0
|
|
CA
|
A:ALA182
|
4.1
|
14.9
|
1.0
|
|
O
|
A:HOH720
|
4.1
|
30.5
|
1.0
|
|
O
|
A:ASP180
|
4.1
|
16.5
|
1.0
|
|
OG
|
A:SER155
|
4.3
|
17.7
|
1.0
|
|
HA
|
A:ASP180
|
4.3
|
15.1
|
1.0
|
|
HA
|
A:ALA182
|
4.4
|
14.8
|
1.0
|
|
O
|
A:HOH751
|
4.4
|
34.1
|
1.0
|
|
HD21
|
A:LEU177
|
4.4
|
15.6
|
1.0
|
|
CA
|
A:ASP180
|
4.5
|
15.0
|
1.0
|
|
C29
|
A:K5O601
|
4.5
|
14.6
|
1.0
|
|
HB3
|
A:ALA182
|
4.6
|
15.7
|
1.0
|
|
H42
|
A:K5O601
|
4.6
|
13.9
|
1.0
|
|
HA
|
A:SER155
|
4.6
|
15.9
|
1.0
|
|
O
|
A:HOH787
|
4.6
|
26.2
|
1.0
|
|
CB
|
A:HIS181
|
4.7
|
15.7
|
1.0
|
|
HD1
|
A:HIS181
|
4.7
|
17.7
|
0.0
|
|
CD2
|
A:LEU177
|
4.7
|
15.6
|
1.0
|
|
CA
|
A:SER155
|
4.7
|
15.6
|
1.0
|
|
S2
|
A:K5O601
|
4.7
|
14.8
|
1.0
|
|
HE1
|
A:PHE238
|
4.8
|
14.8
|
1.0
|
|
H
|
A:SER178
|
4.9
|
13.7
|
1.0
|
|
N
|
A:ASP180
|
5.0
|
14.2
|
1.0
|
|
O
|
A:SER178
|
5.0
|
14.8
|
1.0
|
|
HA
|
A:LEU177
|
5.0
|
14.1
|
1.0
|
|
Fluorine binding site 2 out
of 3 in 8va6
Go back to
Fluorine Binding Sites List in 8va6
Fluorine binding site 2 out
of 3 in the Menin in Complex with Ziftomenib (Ko-539)
 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 Ziftomenib (Ko-539) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:20.1
occ:1.00
|
F2
|
A:K5O601
|
0.0
|
20.1
|
1.0
|
|
C32
|
A:K5O601
|
1.3
|
18.8
|
1.0
|
|
F1
|
A:K5O601
|
2.1
|
16.8
|
1.0
|
|
F3
|
A:K5O601
|
2.1
|
18.5
|
1.0
|
|
C31
|
A:K5O601
|
2.4
|
15.3
|
1.0
|
|
H44
|
A:K5O601
|
2.7
|
15.3
|
1.0
|
|
C30
|
A:K5O601
|
2.9
|
12.8
|
1.0
|
|
HG
|
A:SER155
|
3.1
|
17.7
|
0.0
|
|
HB3
|
A:SER155
|
3.2
|
17.0
|
1.0
|
|
H43
|
A:K5O601
|
3.2
|
15.3
|
1.0
|
|
H42
|
A:K5O601
|
3.3
|
13.9
|
1.0
|
|
C29
|
A:K5O601
|
3.3
|
14.6
|
1.0
|
|
O
|
A:HOH751
|
3.4
|
34.1
|
1.0
|
|
OG
|
A:SER155
|
3.7
|
17.7
|
1.0
|
|
CB
|
A:SER155
|
3.8
|
17.2
|
1.0
|
|
O
|
A:HOH960
|
3.8
|
38.0
|
1.0
|
|
O
|
A:HOH787
|
3.9
|
26.2
|
1.0
|
|
H11
|
A:DMS610
|
3.9
|
46.0
|
1.0
|
|
HB2
|
A:SER155
|
4.0
|
17.0
|
1.0
|
|
S2
|
A:K5O601
|
4.1
|
14.8
|
1.0
|
|
HE1
|
A:PHE238
|
4.2
|
14.8
|
1.0
|
|
HA
|
A:ASP180
|
4.2
|
15.1
|
1.0
|
|
H12
|
A:DMS610
|
4.3
|
46.3
|
1.0
|
|
C28
|
A:K5O601
|
4.4
|
13.4
|
1.0
|
|
C1
|
A:DMS610
|
4.5
|
44.0
|
1.0
|
|
N
|
A:HIS181
|
4.6
|
14.4
|
1.0
|
|
HB1
|
A:ALA182
|
4.6
|
15.7
|
1.0
|
|
S
|
A:DMS610
|
4.6
|
55.7
|
1.0
|
|
HA
|
A:HIS181
|
4.6
|
15.1
|
1.0
|
|
C
|
A:ASP180
|
4.6
|
14.7
|
1.0
|
|
H
|
A:HIS181
|
4.6
|
14.6
|
1.0
|
|
HD22
|
A:LEU177
|
4.7
|
15.6
|
1.0
|
|
C33
|
A:K5O601
|
4.8
|
14.6
|
1.0
|
|
CA
|
A:ASP180
|
4.9
|
15.0
|
1.0
|
|
HZ
|
A:PHE238
|
4.9
|
15.2
|
1.0
|
|
O
|
A:HOH825
|
5.0
|
20.1
|
1.0
|
|
O
|
A:HOH1042
|
5.0
|
58.3
|
1.0
|
|
CA
|
A:HIS181
|
5.0
|
15.1
|
1.0
|
|
C
|
A:HIS181
|
5.0
|
14.9
|
1.0
|
|
O
|
A:ASP180
|
5.0
|
16.5
|
1.0
|
|
O
|
A:HIS181
|
5.0
|
14.0
|
1.0
|
|
Fluorine binding site 3 out
of 3 in 8va6
Go back to
Fluorine Binding Sites List in 8va6
Fluorine binding site 3 out
of 3 in the Menin in Complex with Ziftomenib (Ko-539)
 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 Ziftomenib (Ko-539) within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:18.5
occ:1.00
|
F3
|
A:K5O601
|
0.0
|
18.5
|
1.0
|
|
C32
|
A:K5O601
|
1.3
|
18.8
|
1.0
|
|
F2
|
A:K5O601
|
2.1
|
20.1
|
1.0
|
|
F1
|
A:K5O601
|
2.1
|
16.8
|
1.0
|
|
C31
|
A:K5O601
|
2.3
|
15.3
|
1.0
|
|
H43
|
A:K5O601
|
2.5
|
15.3
|
1.0
|
|
HE1
|
A:PHE238
|
2.7
|
14.8
|
1.0
|
|
HD22
|
A:LEU177
|
2.7
|
15.6
|
1.0
|
|
HB2
|
A:SER155
|
2.9
|
17.0
|
1.0
|
|
C30
|
A:K5O601
|
2.9
|
12.8
|
1.0
|
|
HB3
|
A:SER155
|
2.9
|
17.0
|
1.0
|
|
HG
|
A:SER155
|
3.0
|
17.7
|
0.0
|
|
HB1
|
A:ALA182
|
3.1
|
15.7
|
1.0
|
|
H44
|
A:K5O601
|
3.1
|
15.3
|
1.0
|
|
CB
|
A:SER155
|
3.3
|
17.2
|
1.0
|
|
S2
|
A:K5O601
|
3.3
|
14.8
|
1.0
|
|
CE1
|
A:PHE238
|
3.5
|
14.3
|
1.0
|
|
CD2
|
A:LEU177
|
3.5
|
15.6
|
1.0
|
|
OG
|
A:SER155
|
3.6
|
17.7
|
1.0
|
|
HZ
|
A:PHE238
|
3.6
|
15.2
|
1.0
|
|
HD21
|
A:LEU177
|
3.7
|
15.6
|
1.0
|
|
H11
|
A:DMS610
|
3.7
|
46.0
|
1.0
|
|
HD23
|
A:LEU177
|
3.7
|
15.6
|
1.0
|
|
C29
|
A:K5O601
|
3.9
|
14.6
|
1.0
|
|
CZ
|
A:PHE238
|
4.0
|
15.5
|
1.0
|
|
CB
|
A:ALA182
|
4.0
|
16.0
|
1.0
|
|
O
|
A:HIS181
|
4.2
|
14.0
|
1.0
|
|
HB2
|
A:ALA182
|
4.3
|
15.7
|
1.0
|
|
H42
|
A:K5O601
|
4.4
|
13.9
|
1.0
|
|
C
|
A:HIS181
|
4.5
|
14.9
|
1.0
|
|
HB3
|
A:ALA182
|
4.5
|
15.7
|
1.0
|
|
C1
|
A:DMS610
|
4.5
|
44.0
|
1.0
|
|
HB3
|
A:LEU177
|
4.5
|
14.9
|
1.0
|
|
CD1
|
A:PHE238
|
4.6
|
15.1
|
1.0
|
|
C33
|
A:K5O601
|
4.6
|
14.6
|
1.0
|
|
HD1
|
A:PHE238
|
4.7
|
14.8
|
1.0
|
|
CA
|
A:SER155
|
4.7
|
15.6
|
1.0
|
|
H12
|
A:DMS610
|
4.7
|
46.3
|
1.0
|
|
H23
|
A:DMS610
|
4.7
|
38.0
|
1.0
|
|
CG
|
A:LEU177
|
4.7
|
15.8
|
1.0
|
|
HA
|
A:SER155
|
4.8
|
15.9
|
1.0
|
|
N
|
A:ALA182
|
4.8
|
13.8
|
1.0
|
|
C28
|
A:K5O601
|
4.8
|
13.4
|
1.0
|
|
HD13
|
A:LEU177
|
4.8
|
16.0
|
1.0
|
|
CA
|
A:ALA182
|
4.9
|
14.9
|
1.0
|
|
S
|
A:DMS610
|
4.9
|
55.7
|
1.0
|
|
H
|
A:HIS181
|
4.9
|
14.6
|
1.0
|
|
HA
|
A:LEU177
|
4.9
|
14.1
|
1.0
|
|
HA
|
A:ALA182
|
4.9
|
14.8
|
1.0
|
|
HA
|
A:HIS181
|
4.9
|
15.1
|
1.0
|
|
Reference:
B.D.Clegg,
B.M.Linhares,
T.Cierpicki,
J.Grembecka.
Menin in Complex with Ziftomenib (Ko-539) To Be Published.
Page generated: Wed Jul 16 09:42:24 2025
|
