Fluorine in PDB 6hr2: Crystal Structure of Protac 2 in Complex with the Bromodomain of Human SMARCA4 and Pvhl:Elonginc:Elonginb
Protein crystallography data
The structure of Crystal Structure of Protac 2 in Complex with the Bromodomain of Human SMARCA4 and Pvhl:Elonginc:Elonginb, PDB code: 6hr2
was solved by
M.Roy,
G.Bader,
E.Diers,
N.Trainor,
W.Farnaby,
A.Ciulli,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
39.80 /
1.76
|
Space group
|
P 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
60.332,
61.678,
81.603,
69.43,
83.38,
86.42
|
R / Rfree (%)
|
21.6 /
23.6
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Crystal Structure of Protac 2 in Complex with the Bromodomain of Human SMARCA4 and Pvhl:Elonginc:Elonginb
(pdb code 6hr2). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the
Crystal Structure of Protac 2 in Complex with the Bromodomain of Human SMARCA4 and Pvhl:Elonginc:Elonginb, PDB code: 6hr2:
Jump to Fluorine binding site number:
1;
2;
Fluorine binding site 1 out
of 2 in 6hr2
Go back to
Fluorine Binding Sites List in 6hr2
Fluorine binding site 1 out
of 2 in the Crystal Structure of Protac 2 in Complex with the Bromodomain of Human SMARCA4 and Pvhl:Elonginc:Elonginb
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Crystal Structure of Protac 2 in Complex with the Bromodomain of Human SMARCA4 and Pvhl:Elonginc:Elonginb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F301
b:34.0
occ:1.00
|
F34
|
B:FWZ301
|
0.0
|
34.0
|
1.0
|
C32
|
B:FWZ301
|
1.4
|
34.4
|
1.0
|
H1
|
B:FWZ301
|
2.2
|
34.5
|
0.0
|
C35
|
B:FWZ301
|
2.4
|
34.1
|
1.0
|
C36
|
B:FWZ301
|
2.4
|
32.4
|
1.0
|
C31
|
B:FWZ301
|
2.4
|
34.5
|
1.0
|
HA
|
A:ASN1540
|
2.5
|
29.7
|
0.0
|
H30
|
B:FWZ301
|
2.6
|
34.1
|
0.0
|
H31
|
B:FWZ301
|
2.6
|
32.4
|
0.0
|
N1
|
B:FWZ301
|
2.7
|
34.5
|
1.0
|
OH
|
B:TYR112
|
3.3
|
34.3
|
1.0
|
O
|
A:PHE1539
|
3.3
|
32.3
|
1.0
|
H29
|
B:FWZ301
|
3.4
|
34.1
|
0.0
|
H32
|
B:FWZ301
|
3.4
|
32.4
|
0.0
|
HE2
|
A:PHE1539
|
3.4
|
34.3
|
0.0
|
CE2
|
A:PHE1539
|
3.4
|
34.4
|
1.0
|
OD1
|
A:ASN1540
|
3.4
|
31.6
|
1.0
|
HH
|
B:TYR112
|
3.6
|
34.3
|
0.0
|
O33
|
B:FWZ301
|
3.6
|
31.6
|
1.0
|
CA
|
A:ASN1540
|
3.6
|
29.7
|
1.0
|
H9
|
B:FWZ301
|
3.6
|
31.6
|
0.0
|
CD2
|
A:PHE1539
|
3.6
|
31.7
|
1.0
|
CZ
|
B:TYR112
|
3.7
|
33.5
|
1.0
|
HD2
|
A:PHE1539
|
3.7
|
31.6
|
0.0
|
C
|
A:PHE1539
|
3.9
|
31.6
|
1.0
|
CZ
|
A:PHE1539
|
4.0
|
32.2
|
1.0
|
CG
|
A:ASN1540
|
4.1
|
46.5
|
1.0
|
C2
|
B:FWZ301
|
4.1
|
33.0
|
1.0
|
N
|
A:ASN1540
|
4.1
|
28.8
|
1.0
|
H50
|
B:FWZ301
|
4.2
|
30.4
|
0.0
|
CE1
|
B:TYR112
|
4.2
|
26.7
|
1.0
|
CE2
|
B:TYR112
|
4.2
|
27.9
|
1.0
|
H6
|
B:FWZ301
|
4.2
|
32.5
|
0.0
|
CB
|
A:ASN1540
|
4.3
|
27.7
|
1.0
|
O
|
A:HOH1601
|
4.3
|
34.3
|
1.0
|
HH22
|
B:ARG69
|
4.3
|
29.7
|
0.0
|
HE1
|
B:TYR112
|
4.3
|
26.7
|
0.0
|
O
|
A:ASN1540
|
4.3
|
33.1
|
1.0
|
O9
|
B:FWZ301
|
4.3
|
32.9
|
1.0
|
HE2
|
B:TYR112
|
4.3
|
27.9
|
0.0
|
CG
|
A:PHE1539
|
4.3
|
30.5
|
1.0
|
HB3
|
A:ASN1540
|
4.4
|
27.7
|
0.0
|
HZ
|
A:PHE1539
|
4.4
|
32.2
|
0.0
|
C
|
A:ASN1540
|
4.4
|
34.0
|
1.0
|
C7
|
B:FWZ301
|
4.5
|
31.6
|
1.0
|
CE1
|
A:PHE1539
|
4.6
|
33.8
|
1.0
|
C4
|
B:FWZ301
|
4.7
|
32.5
|
1.0
|
H17
|
B:FWZ301
|
4.7
|
33.1
|
0.0
|
HH21
|
B:ARG69
|
4.8
|
30.0
|
0.0
|
C3
|
B:FWZ301
|
4.8
|
33.5
|
1.0
|
H8
|
B:FWZ301
|
4.8
|
31.7
|
0.0
|
CD1
|
A:PHE1539
|
4.8
|
32.9
|
1.0
|
NH2
|
B:ARG69
|
4.9
|
29.8
|
1.0
|
H
|
A:ASN1540
|
5.0
|
28.8
|
0.0
|
C6
|
B:FWZ301
|
5.0
|
32.5
|
1.0
|
|
Fluorine binding site 2 out
of 2 in 6hr2
Go back to
Fluorine Binding Sites List in 6hr2
Fluorine binding site 2 out
of 2 in the Crystal Structure of Protac 2 in Complex with the Bromodomain of Human SMARCA4 and Pvhl:Elonginc:Elonginb
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Crystal Structure of Protac 2 in Complex with the Bromodomain of Human SMARCA4 and Pvhl:Elonginc:Elonginb within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
F:F301
b:27.6
occ:1.00
|
F34
|
F:FWZ301
|
0.0
|
27.6
|
1.0
|
C32
|
F:FWZ301
|
1.4
|
26.0
|
1.0
|
H1
|
F:FWZ301
|
2.2
|
24.1
|
0.0
|
C31
|
F:FWZ301
|
2.4
|
25.5
|
1.0
|
C36
|
F:FWZ301
|
2.4
|
23.9
|
1.0
|
C35
|
F:FWZ301
|
2.4
|
23.7
|
1.0
|
HA
|
E:ASN1540
|
2.5
|
24.4
|
0.0
|
N1
|
F:FWZ301
|
2.6
|
24.1
|
1.0
|
H31
|
F:FWZ301
|
2.6
|
23.8
|
0.0
|
H30
|
F:FWZ301
|
2.6
|
23.7
|
0.0
|
HE2
|
E:PHE1539
|
3.2
|
30.8
|
0.0
|
CE2
|
E:PHE1539
|
3.2
|
30.8
|
1.0
|
O
|
E:PHE1539
|
3.3
|
26.3
|
1.0
|
OH
|
F:TYR112
|
3.3
|
27.1
|
1.0
|
OD1
|
E:ASN1540
|
3.4
|
26.5
|
1.0
|
H32
|
F:FWZ301
|
3.4
|
23.9
|
0.0
|
H29
|
F:FWZ301
|
3.4
|
23.8
|
0.0
|
CD2
|
E:PHE1539
|
3.4
|
27.8
|
1.0
|
O33
|
F:FWZ301
|
3.5
|
24.9
|
1.0
|
H9
|
F:FWZ301
|
3.6
|
27.7
|
0.0
|
HD2
|
E:PHE1539
|
3.6
|
27.8
|
0.0
|
CA
|
E:ASN1540
|
3.6
|
24.3
|
1.0
|
HH
|
F:TYR112
|
3.6
|
27.1
|
0.0
|
CZ
|
F:TYR112
|
3.7
|
26.6
|
1.0
|
CZ
|
E:PHE1539
|
3.8
|
29.0
|
1.0
|
C
|
E:PHE1539
|
3.8
|
27.6
|
1.0
|
CG
|
E:ASN1540
|
4.0
|
39.1
|
1.0
|
N
|
E:ASN1540
|
4.1
|
25.2
|
1.0
|
C2
|
F:FWZ301
|
4.1
|
24.6
|
1.0
|
H50
|
F:FWZ301
|
4.1
|
29.8
|
0.0
|
CE1
|
F:TYR112
|
4.2
|
23.3
|
1.0
|
O
|
E:HOH1701
|
4.2
|
27.6
|
1.0
|
CG
|
E:PHE1539
|
4.2
|
26.3
|
1.0
|
HZ
|
E:PHE1539
|
4.2
|
29.0
|
0.0
|
HE1
|
F:TYR112
|
4.2
|
23.2
|
0.0
|
H6
|
F:FWZ301
|
4.3
|
28.7
|
0.0
|
O9
|
F:FWZ301
|
4.3
|
24.5
|
1.0
|
CB
|
E:ASN1540
|
4.3
|
24.1
|
1.0
|
CE2
|
F:TYR112
|
4.3
|
23.9
|
1.0
|
HB3
|
E:ASN1540
|
4.4
|
24.1
|
0.0
|
O
|
E:ASN1540
|
4.4
|
26.1
|
1.0
|
HH22
|
F:ARG69
|
4.5
|
31.6
|
0.0
|
C
|
E:ASN1540
|
4.5
|
27.7
|
1.0
|
C7
|
F:FWZ301
|
4.5
|
27.6
|
1.0
|
CE1
|
E:PHE1539
|
4.5
|
29.9
|
1.0
|
HE2
|
F:TYR112
|
4.5
|
23.9
|
0.0
|
C4
|
F:FWZ301
|
4.6
|
23.9
|
1.0
|
CD1
|
E:PHE1539
|
4.6
|
28.9
|
1.0
|
HE1
|
F:HIS110
|
4.7
|
29.7
|
0.0
|
H17
|
F:FWZ301
|
4.7
|
24.6
|
0.0
|
H8
|
F:FWZ301
|
4.8
|
27.6
|
0.0
|
C3
|
F:FWZ301
|
4.8
|
29.4
|
1.0
|
HH21
|
F:ARG69
|
4.8
|
31.7
|
0.0
|
H
|
E:ASN1540
|
4.9
|
25.2
|
0.0
|
ND2
|
E:ASN1540
|
5.0
|
31.3
|
1.0
|
CA
|
E:PHE1539
|
5.0
|
24.2
|
1.0
|
|
Reference:
W.Farnaby,
M.Koegl,
M.J.Roy,
C.Whitworth,
E.Diers,
N.Trainor,
D.Zollman,
S.Steurer,
J.Karolyi-Oezguer,
C.Riedmueller,
T.Gmaschitz,
J.Wachter,
C.Dank,
M.Galant,
B.Sharps,
K.Rumpel,
E.Traxler,
T.Gerstberger,
R.Schnitzer,
O.Petermann,
P.Greb,
H.Weinstabl,
G.Bader,
A.Zoephel,
A.Weiss-Puxbaum,
K.Ehrenhofer-Wolfer,
S.Wohrle,
G.Boehmelt,
J.Rinnenthal,
H.Arnhof,
N.Wiechens,
M.Y.Wu,
T.Owen-Hughes,
P.Ettmayer,
M.Pearson,
D.B.Mcconnell,
A.Ciulli.
Baf Complex Vulnerabilities in Cancer Demonstrated Via Structure-Based Protac Design. Nat.Chem.Biol. V. 15 672 2019.
ISSN: ESSN 1552-4469
PubMed: 31178587
DOI: 10.1038/S41589-019-0294-6
Page generated: Sun Dec 13 12:53:50 2020
|