Fluorine in PDB 5ddc: Menin in Complex with Mi-2-3
Protein crystallography data
The structure of Menin in Complex with Mi-2-3, PDB code: 5ddc
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)
|
38.74 /
1.62
|
Space group
|
P 21 21 21
|
Cell size a, b, c (Å), α, β, γ (°)
|
49.445,
80.253,
124.456,
90.00,
90.00,
90.00
|
R / Rfree (%)
|
15.9 /
19.4
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Menin in Complex with Mi-2-3
(pdb code 5ddc). 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-2-3, PDB code: 5ddc:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
Fluorine binding site 1 out
of 6 in 5ddc
Go back to
Fluorine Binding Sites List in 5ddc
Fluorine binding site 1 out
of 6 in the Menin in Complex with Mi-2-3
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-2-3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:9.8
occ:1.00
|
FAA
|
A:59V601
|
0.0
|
9.8
|
1.0
|
CBB
|
A:59V601
|
1.3
|
7.9
|
1.0
|
FAB
|
A:59V601
|
2.2
|
7.1
|
1.0
|
FAC
|
A:59V601
|
2.2
|
8.1
|
1.0
|
CAM
|
A:59V601
|
2.4
|
6.7
|
1.0
|
CAT
|
A:59V601
|
2.9
|
6.8
|
1.0
|
O
|
A:HOH1119
|
3.1
|
19.4
|
1.0
|
C1
|
A:DMS604
|
3.4
|
22.4
|
0.5
|
OG
|
A:SER155
|
3.4
|
7.4
|
1.0
|
CAH
|
A:59V601
|
3.4
|
6.4
|
1.0
|
O
|
A:HOH1165
|
3.6
|
23.2
|
1.0
|
CB
|
A:SER155
|
3.6
|
5.5
|
1.0
|
S
|
A:DMS602
|
3.6
|
10.9
|
0.5
|
O
|
A:HOH1138
|
3.8
|
40.3
|
1.0
|
O
|
A:DMS602
|
3.8
|
12.2
|
0.5
|
O
|
A:HOH857
|
3.9
|
12.4
|
1.0
|
SAS
|
A:59V601
|
4.0
|
8.2
|
1.0
|
C2
|
A:DMS602
|
4.1
|
12.5
|
0.5
|
C5
|
A:59V601
|
4.4
|
6.9
|
1.0
|
C4
|
A:59V601
|
4.7
|
7.9
|
1.0
|
CE1
|
A:PHE238
|
4.7
|
5.5
|
1.0
|
N
|
A:HIS181
|
4.8
|
3.6
|
1.0
|
S
|
A:DMS604
|
4.9
|
22.5
|
0.5
|
C
|
A:ASP180
|
5.0
|
4.8
|
1.0
|
CA
|
A:SER155
|
5.0
|
5.2
|
1.0
|
|
Fluorine binding site 2 out
of 6 in 5ddc
Go back to
Fluorine Binding Sites List in 5ddc
Fluorine binding site 2 out
of 6 in the Menin in Complex with Mi-2-3
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-2-3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:7.1
occ:1.00
|
FAB
|
A:59V601
|
0.0
|
7.1
|
1.0
|
CBB
|
A:59V601
|
1.3
|
7.9
|
1.0
|
FAA
|
A:59V601
|
2.2
|
9.8
|
1.0
|
FAC
|
A:59V601
|
2.2
|
8.1
|
1.0
|
CAM
|
A:59V601
|
2.4
|
6.7
|
1.0
|
C
|
A:HIS181
|
3.0
|
5.8
|
1.0
|
CA
|
A:HIS181
|
3.0
|
3.7
|
1.0
|
N
|
A:HIS181
|
3.1
|
3.6
|
1.0
|
O
|
A:HOH1165
|
3.1
|
23.2
|
1.0
|
O
|
A:HIS181
|
3.2
|
5.1
|
1.0
|
N
|
A:ALA182
|
3.5
|
5.3
|
1.0
|
C
|
A:ASP180
|
3.5
|
4.8
|
1.0
|
O
|
A:HOH1119
|
3.6
|
19.4
|
1.0
|
CAT
|
A:59V601
|
3.7
|
6.8
|
1.0
|
CB
|
A:SER155
|
3.8
|
5.5
|
1.0
|
O
|
A:HOH728
|
3.8
|
20.3
|
1.0
|
O
|
A:ASP180
|
3.9
|
6.6
|
1.0
|
CB
|
A:ALA182
|
4.0
|
4.8
|
1.0
|
CA
|
A:ALA182
|
4.3
|
3.1
|
1.0
|
OG
|
A:SER155
|
4.4
|
7.4
|
1.0
|
CA
|
A:ASP180
|
4.4
|
5.3
|
1.0
|
CB
|
A:HIS181
|
4.5
|
3.7
|
1.0
|
O
|
A:HOH857
|
4.6
|
12.4
|
1.0
|
CAH
|
A:59V601
|
4.7
|
6.4
|
1.0
|
SAS
|
A:59V601
|
4.7
|
8.2
|
1.0
|
CA
|
A:SER155
|
4.8
|
5.2
|
1.0
|
N
|
A:ASP180
|
4.9
|
4.6
|
1.0
|
O
|
A:SER178
|
5.0
|
4.9
|
1.0
|
|
Fluorine binding site 3 out
of 6 in 5ddc
Go back to
Fluorine Binding Sites List in 5ddc
Fluorine binding site 3 out
of 6 in the Menin in Complex with Mi-2-3
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-2-3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:8.1
occ:1.00
|
FAC
|
A:59V601
|
0.0
|
8.1
|
1.0
|
CBB
|
A:59V601
|
1.3
|
7.9
|
1.0
|
FAA
|
A:59V601
|
2.2
|
9.8
|
1.0
|
FAB
|
A:59V601
|
2.2
|
7.1
|
1.0
|
CAM
|
A:59V601
|
2.4
|
6.7
|
1.0
|
CAT
|
A:59V601
|
2.9
|
6.8
|
1.0
|
SAS
|
A:59V601
|
3.1
|
8.2
|
1.0
|
CB
|
A:SER155
|
3.4
|
5.5
|
1.0
|
CD2
|
A:LEU177
|
3.5
|
6.4
|
1.0
|
CE1
|
A:PHE238
|
3.6
|
5.5
|
1.0
|
CB
|
A:ALA182
|
3.8
|
4.8
|
1.0
|
O
|
A:HIS181
|
3.8
|
5.1
|
1.0
|
OG
|
A:SER155
|
3.9
|
7.4
|
1.0
|
CAH
|
A:59V601
|
4.0
|
6.4
|
1.0
|
C
|
A:HIS181
|
4.1
|
5.8
|
1.0
|
CZ
|
A:PHE238
|
4.2
|
6.2
|
1.0
|
C1
|
A:DMS604
|
4.3
|
22.4
|
0.5
|
S
|
A:DMS602
|
4.3
|
10.9
|
0.5
|
N
|
A:ALA182
|
4.4
|
5.3
|
1.0
|
C4
|
A:59V601
|
4.5
|
7.9
|
1.0
|
CA
|
A:ALA182
|
4.5
|
3.1
|
1.0
|
CD1
|
A:PHE238
|
4.6
|
5.1
|
1.0
|
N
|
A:HIS181
|
4.7
|
3.6
|
1.0
|
CA
|
A:HIS181
|
4.7
|
3.7
|
1.0
|
CG
|
A:LEU177
|
4.8
|
7.0
|
1.0
|
CA
|
A:SER155
|
4.8
|
5.2
|
1.0
|
C5
|
A:59V601
|
4.8
|
6.9
|
1.0
|
O
|
A:HOH1165
|
4.9
|
23.2
|
1.0
|
O
|
A:SER178
|
4.9
|
4.9
|
1.0
|
C2
|
A:DMS602
|
4.9
|
12.5
|
0.5
|
O
|
A:HOH1119
|
4.9
|
19.4
|
1.0
|
CB
|
A:LEU177
|
5.0
|
6.4
|
1.0
|
|
Fluorine binding site 4 out
of 6 in 5ddc
Go back to
Fluorine Binding Sites List in 5ddc
Fluorine binding site 4 out
of 6 in the Menin in Complex with Mi-2-3
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-2-3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:20.0
occ:1.00
|
FAE
|
A:59V601
|
0.0
|
20.0
|
1.0
|
CBC
|
A:59V601
|
1.3
|
17.1
|
0.9
|
FAD
|
A:59V601
|
2.2
|
15.0
|
0.8
|
FAF
|
A:59V601
|
2.2
|
21.2
|
1.0
|
CAV
|
A:59V601
|
2.3
|
9.2
|
1.0
|
SAR
|
A:59V601
|
3.3
|
10.9
|
1.0
|
NAQ
|
A:59V601
|
3.3
|
12.1
|
1.0
|
CB
|
A:MET322
|
3.4
|
7.9
|
0.5
|
CB
|
A:MET322
|
3.6
|
5.1
|
0.5
|
O
|
A:HOH1000
|
3.8
|
24.1
|
1.0
|
O
|
A:HOH716
|
3.9
|
18.2
|
0.5
|
CD1
|
A:TYR319
|
3.9
|
6.8
|
1.0
|
OE2
|
A:GLU363
|
4.1
|
45.2
|
0.5
|
CE1
|
A:TYR319
|
4.2
|
7.1
|
1.0
|
CG
|
A:MET322
|
4.2
|
17.4
|
0.5
|
SD
|
A:MET322
|
4.2
|
4.7
|
0.5
|
NAP
|
A:59V601
|
4.3
|
14.1
|
1.0
|
C
|
A:MET322
|
4.3
|
6.9
|
1.0
|
CAU
|
A:59V601
|
4.4
|
9.2
|
1.0
|
CA
|
A:MET322
|
4.5
|
5.6
|
0.5
|
O
|
A:MET322
|
4.5
|
5.7
|
1.0
|
CG
|
A:MET322
|
4.5
|
5.7
|
0.5
|
CA
|
A:MET322
|
4.6
|
4.4
|
0.5
|
N
|
A:TYR323
|
4.6
|
5.5
|
1.0
|
CD
|
A:GLU363
|
4.7
|
25.6
|
0.5
|
O
|
A:HOH1012
|
4.7
|
22.9
|
1.0
|
CG
|
A:TYR319
|
4.8
|
4.4
|
1.0
|
SD
|
A:MET322
|
4.8
|
15.5
|
0.5
|
O
|
A:HOH1073
|
4.9
|
19.9
|
1.0
|
OE1
|
A:GLU363
|
4.9
|
21.8
|
0.5
|
|
Fluorine binding site 5 out
of 6 in 5ddc
Go back to
Fluorine Binding Sites List in 5ddc
Fluorine binding site 5 out
of 6 in the Menin in Complex with Mi-2-3
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-2-3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:21.2
occ:1.00
|
FAF
|
A:59V601
|
0.0
|
21.2
|
1.0
|
CBC
|
A:59V601
|
1.3
|
17.1
|
0.9
|
FAD
|
A:59V601
|
2.2
|
15.0
|
0.8
|
FAE
|
A:59V601
|
2.2
|
20.0
|
1.0
|
CAV
|
A:59V601
|
2.3
|
9.2
|
1.0
|
NAQ
|
A:59V601
|
2.7
|
12.1
|
1.0
|
O
|
A:HOH1073
|
3.1
|
19.9
|
1.0
|
O
|
A:HOH1000
|
3.2
|
24.1
|
1.0
|
O
|
A:HOH883
|
3.4
|
17.1
|
1.0
|
CA
|
A:TYR323
|
3.6
|
6.1
|
1.0
|
O
|
A:MET322
|
3.7
|
5.7
|
1.0
|
N
|
A:TYR323
|
3.7
|
5.5
|
1.0
|
C
|
A:MET322
|
3.7
|
6.9
|
1.0
|
CD1
|
A:TYR323
|
3.8
|
6.4
|
1.0
|
SAR
|
A:59V601
|
3.8
|
10.9
|
1.0
|
CG
|
A:TYR323
|
4.0
|
5.5
|
1.0
|
NAP
|
A:59V601
|
4.0
|
14.1
|
1.0
|
CB
|
A:MET322
|
4.2
|
7.9
|
0.5
|
O
|
A:HOH848
|
4.2
|
10.3
|
1.0
|
CE1
|
A:TYR323
|
4.3
|
7.9
|
1.0
|
CB
|
A:MET322
|
4.3
|
5.1
|
0.5
|
CB
|
A:TYR323
|
4.4
|
6.8
|
1.0
|
CAU
|
A:59V601
|
4.6
|
9.2
|
1.0
|
CA
|
A:MET322
|
4.6
|
5.6
|
0.5
|
CD2
|
A:TYR323
|
4.7
|
8.1
|
1.0
|
CA
|
A:MET322
|
4.7
|
4.4
|
0.5
|
C
|
A:TYR323
|
4.8
|
6.0
|
1.0
|
O
|
A:HOH1012
|
4.9
|
22.9
|
1.0
|
CZ
|
A:TYR323
|
4.9
|
7.5
|
1.0
|
O
|
A:TYR323
|
5.0
|
6.3
|
1.0
|
|
Fluorine binding site 6 out
of 6 in 5ddc
Go back to
Fluorine Binding Sites List in 5ddc
Fluorine binding site 6 out
of 6 in the Menin in Complex with Mi-2-3
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-2-3 within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F601
b:15.0
occ:0.80
|
FAD
|
A:59V601
|
0.0
|
15.0
|
0.8
|
CBC
|
A:59V601
|
1.3
|
17.1
|
0.9
|
FAE
|
A:59V601
|
2.2
|
20.0
|
1.0
|
FAF
|
A:59V601
|
2.2
|
21.2
|
1.0
|
CAV
|
A:59V601
|
2.3
|
9.2
|
1.0
|
CB
|
A:MET322
|
3.0
|
7.9
|
0.5
|
SAR
|
A:59V601
|
3.0
|
10.9
|
1.0
|
N
|
A:TYR323
|
3.0
|
5.5
|
1.0
|
CB
|
A:MET322
|
3.2
|
5.1
|
0.5
|
O
|
A:TYR319
|
3.3
|
6.7
|
1.0
|
C
|
A:MET322
|
3.4
|
6.9
|
1.0
|
NAQ
|
A:59V601
|
3.5
|
12.1
|
1.0
|
CG
|
A:TYR323
|
3.6
|
5.5
|
1.0
|
CD2
|
A:TYR323
|
3.6
|
8.1
|
1.0
|
CA
|
A:TYR323
|
3.6
|
6.1
|
1.0
|
CD1
|
A:TYR319
|
3.7
|
6.8
|
1.0
|
CB
|
A:TYR319
|
3.8
|
5.2
|
1.0
|
CA
|
A:MET322
|
3.8
|
5.6
|
0.5
|
CA
|
A:MET322
|
3.8
|
4.4
|
0.5
|
CE2
|
A:TYR323
|
3.9
|
8.8
|
1.0
|
CD1
|
A:TYR323
|
4.0
|
6.4
|
1.0
|
CA
|
A:TYR319
|
4.0
|
4.1
|
1.0
|
O
|
A:MET322
|
4.0
|
5.7
|
1.0
|
CG
|
A:TYR319
|
4.0
|
4.4
|
1.0
|
C
|
A:TYR319
|
4.0
|
5.3
|
1.0
|
CB
|
A:TYR323
|
4.1
|
6.8
|
1.0
|
CG
|
A:MET322
|
4.3
|
17.4
|
0.5
|
CZ
|
A:TYR323
|
4.3
|
7.5
|
1.0
|
CE1
|
A:TYR323
|
4.3
|
7.9
|
1.0
|
CAU
|
A:59V601
|
4.4
|
9.2
|
1.0
|
NAP
|
A:59V601
|
4.5
|
14.1
|
1.0
|
N
|
A:MET322
|
4.5
|
4.3
|
1.0
|
CG
|
A:MET322
|
4.6
|
5.7
|
0.5
|
CE1
|
A:TYR319
|
4.6
|
7.1
|
1.0
|
O
|
A:HOH1000
|
4.6
|
24.1
|
1.0
|
SD
|
A:MET322
|
4.9
|
4.7
|
0.5
|
|
Reference:
J.Pollock,
D.Borkin,
G.Lund,
T.Purohit,
E.Dyguda-Kazimierowicz,
J.Grembecka,
T.Cierpicki.
Rational Design of Orthogonal Multipolar Interactions with Fluorine in Protein-Ligand Complexes. J.Med.Chem. V. 58 7465 2015.
ISSN: ISSN 0022-2623
PubMed: 26288158
DOI: 10.1021/ACS.JMEDCHEM.5B00975
Page generated: Thu Aug 1 08:42:25 2024
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