Fluorine in PDB 5rc3: Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library F03A
Enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library F03A
All present enzymatic activity of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library F03A:
3.4.23.22;
Protein crystallography data
The structure of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library F03A, PDB code: 5rc3
was solved by
M.S.Weiss,
J.Wollenhaupt,
A.Metz,
T.Barthel,
G.M.A.Lima,
A.Heine,
U.Mueller,
G.Klebe,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
|
Resolution Low / High (Å)
|
42.86 /
0.98
|
|
Space group
|
P 1 21 1
|
|
Cell size a, b, c (Å), α, β, γ (°)
|
45.349,
72.941,
52.592,
90.00,
109.22,
90.00
|
|
R / Rfree (%)
|
16.3 /
16.3
|
Fluorine Binding Sites:
The binding sites of Fluorine atom in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library F03A
(pdb code 5rc3). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 2 binding sites of Fluorine where determined in the
Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library F03A, PDB code: 5rc3:
Jump to Fluorine binding site number:
1;
2;
Fluorine binding site 1 out
of 2 in 5rc3
Go back to
Fluorine Binding Sites List in 5rc3
Fluorine binding site 1 out
of 2 in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library F03A
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 1 of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library F03A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:13.7
occ:0.20
|
F
|
A:RAY401
|
0.0
|
13.7
|
0.2
|
|
F
|
A:RAY401
|
0.0
|
13.7
|
0.2
|
|
C9
|
A:RAY401
|
1.4
|
13.1
|
0.2
|
|
C9
|
A:RAY401
|
1.4
|
13.1
|
0.2
|
|
C10
|
A:RAY401
|
2.3
|
13.5
|
0.2
|
|
C10
|
A:RAY401
|
2.3
|
13.5
|
0.2
|
|
C8
|
A:RAY401
|
2.3
|
13.5
|
0.2
|
|
C8
|
A:RAY401
|
2.3
|
13.5
|
0.2
|
|
CD1
|
A:LEU133
|
2.9
|
13.1
|
0.3
|
|
CD1
|
A:LEU133
|
2.9
|
13.1
|
0.3
|
|
O
|
A:HOH635
|
3.1
|
10.9
|
0.3
|
|
O
|
A:HOH635
|
3.1
|
10.9
|
0.3
|
|
O
|
A:HOH635
|
3.3
|
10.5
|
0.2
|
|
O
|
A:HOH635
|
3.3
|
10.5
|
0.2
|
|
CB
|
A:LEU133
|
3.3
|
10.1
|
0.2
|
|
CB
|
A:LEU133
|
3.3
|
10.1
|
0.2
|
|
CD1
|
A:LEU133
|
3.3
|
10.4
|
0.2
|
|
CD1
|
A:LEU133
|
3.3
|
10.4
|
0.2
|
|
CA
|
A:SER38
|
3.4
|
8.9
|
0.3
|
|
CA
|
A:SER38
|
3.4
|
8.9
|
0.3
|
|
CA
|
A:SER38
|
3.4
|
9.3
|
0.2
|
|
CA
|
A:SER38
|
3.4
|
9.3
|
0.2
|
|
CB
|
A:LEU133
|
3.4
|
11.5
|
0.3
|
|
CB
|
A:LEU133
|
3.4
|
11.5
|
0.3
|
|
O
|
A:GLY37
|
3.5
|
9.6
|
0.3
|
|
O
|
A:GLY37
|
3.5
|
9.6
|
0.3
|
|
CG
|
A:LEU133
|
3.6
|
12.7
|
0.3
|
|
CG
|
A:LEU133
|
3.6
|
12.7
|
0.3
|
|
C7
|
A:RAY401
|
3.6
|
14.6
|
0.2
|
|
C7
|
A:RAY401
|
3.6
|
14.6
|
0.2
|
|
C5
|
A:RAY401
|
3.6
|
13.7
|
0.2
|
|
C5
|
A:RAY401
|
3.6
|
13.7
|
0.2
|
|
O
|
A:GLY37
|
3.6
|
9.7
|
0.2
|
|
O
|
A:GLY37
|
3.6
|
9.7
|
0.2
|
|
CB
|
A:SER38
|
3.7
|
9.4
|
0.3
|
|
CB
|
A:SER38
|
3.7
|
9.4
|
0.3
|
|
CB
|
A:SER38
|
3.8
|
9.6
|
0.2
|
|
CB
|
A:SER38
|
3.8
|
9.6
|
0.2
|
|
CG
|
A:LEU133
|
3.9
|
10.5
|
0.2
|
|
CG
|
A:LEU133
|
3.9
|
10.5
|
0.2
|
|
CD2
|
A:LEU133
|
3.9
|
13.6
|
0.3
|
|
CD2
|
A:LEU133
|
3.9
|
13.6
|
0.3
|
|
N
|
A:SER39
|
4.1
|
8.1
|
0.3
|
|
N
|
A:SER39
|
4.1
|
8.1
|
0.3
|
|
C6
|
A:RAY401
|
4.1
|
14.2
|
0.2
|
|
C6
|
A:RAY401
|
4.1
|
14.2
|
0.2
|
|
N
|
A:SER39
|
4.1
|
8.9
|
0.2
|
|
N
|
A:SER39
|
4.1
|
8.9
|
0.2
|
|
C
|
A:SER38
|
4.2
|
8.1
|
0.3
|
|
C
|
A:SER38
|
4.2
|
8.1
|
0.3
|
|
CE2
|
A:PHE194
|
4.2
|
13.6
|
0.2
|
|
CE2
|
A:PHE194
|
4.2
|
13.6
|
0.2
|
|
C
|
A:SER38
|
4.3
|
8.8
|
0.2
|
|
C
|
A:SER38
|
4.3
|
8.8
|
0.2
|
|
O
|
A:LEU133
|
4.3
|
10.9
|
0.3
|
|
O
|
A:LEU133
|
4.3
|
10.9
|
0.3
|
|
C
|
A:GLY37
|
4.3
|
8.6
|
0.3
|
|
C
|
A:GLY37
|
4.3
|
8.6
|
0.3
|
|
N
|
A:SER38
|
4.3
|
8.4
|
0.3
|
|
N
|
A:SER38
|
4.3
|
8.4
|
0.3
|
|
C
|
A:GLY37
|
4.3
|
9.1
|
0.2
|
|
C
|
A:GLY37
|
4.3
|
9.1
|
0.2
|
|
N
|
A:SER38
|
4.3
|
9.0
|
0.2
|
|
N
|
A:SER38
|
4.3
|
9.0
|
0.2
|
|
O
|
A:LEU133
|
4.4
|
11.5
|
0.2
|
|
O
|
A:LEU133
|
4.4
|
11.5
|
0.2
|
|
OG
|
A:SER39
|
4.5
|
8.7
|
0.3
|
|
OG
|
A:SER39
|
4.5
|
8.7
|
0.3
|
|
CE2
|
A:PHE194
|
4.5
|
11.5
|
0.3
|
|
CE2
|
A:PHE194
|
4.5
|
11.5
|
0.3
|
|
CZ
|
A:PHE194
|
4.5
|
13.4
|
0.2
|
|
CZ
|
A:PHE194
|
4.5
|
13.5
|
0.2
|
|
CA
|
A:LEU133
|
4.6
|
10.2
|
0.2
|
|
CA
|
A:LEU133
|
4.6
|
10.2
|
0.2
|
|
CD2
|
A:LEU133
|
4.7
|
10.2
|
0.2
|
|
CD2
|
A:LEU133
|
4.7
|
10.2
|
0.2
|
|
CA
|
A:LEU133
|
4.7
|
10.5
|
0.3
|
|
CA
|
A:LEU133
|
4.7
|
10.5
|
0.3
|
|
N
|
A:RAY401
|
4.7
|
13.9
|
0.2
|
|
N
|
A:RAY401
|
4.7
|
13.9
|
0.2
|
|
C
|
A:LEU133
|
4.8
|
10.1
|
0.2
|
|
C
|
A:LEU133
|
4.8
|
10.1
|
0.2
|
|
O
|
A:HOH541
|
4.8
|
16.0
|
0.2
|
|
O
|
A:HOH541
|
4.8
|
16.0
|
0.2
|
|
CD1
|
A:ILE77
|
4.8
|
12.6
|
0.2
|
|
CD1
|
A:ILE77
|
4.8
|
12.6
|
0.2
|
|
C
|
A:LEU133
|
4.8
|
9.8
|
0.3
|
|
C
|
A:LEU133
|
4.8
|
9.8
|
0.3
|
|
OG
|
A:SER39
|
4.9
|
9.0
|
0.2
|
|
OG
|
A:SER39
|
4.9
|
9.0
|
0.2
|
|
CB
|
A:SER39
|
4.9
|
8.9
|
0.3
|
|
CB
|
A:SER39
|
4.9
|
8.9
|
0.3
|
|
Fluorine binding site 2 out
of 2 in 5rc3
Go back to
Fluorine Binding Sites List in 5rc3
Fluorine binding site 2 out
of 2 in the Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library F03A
 Mono view
 Stereo pair view
|
|
A full contact list of Fluorine with other atoms in the F binding
site number 2 of Pandda Analysis Group Deposition -- Endothiapepsin Changed State Model For Fragment F2X-Entry Library F03A within 5.0Å range:
|
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F401
b:13.7
occ:0.20
|
F
|
A:RAY401
|
0.0
|
13.7
|
0.2
|
|
F
|
A:RAY401
|
0.0
|
13.7
|
0.2
|
|
C9
|
A:RAY401
|
1.4
|
13.1
|
0.2
|
|
C9
|
A:RAY401
|
1.4
|
13.1
|
0.2
|
|
C10
|
A:RAY401
|
2.3
|
13.5
|
0.2
|
|
C10
|
A:RAY401
|
2.3
|
13.5
|
0.2
|
|
C8
|
A:RAY401
|
2.3
|
13.5
|
0.2
|
|
C8
|
A:RAY401
|
2.3
|
13.5
|
0.2
|
|
CD1
|
A:LEU133
|
2.9
|
13.1
|
0.3
|
|
CD1
|
A:LEU133
|
2.9
|
13.1
|
0.3
|
|
O
|
A:HOH635
|
3.1
|
10.9
|
0.3
|
|
O
|
A:HOH635
|
3.1
|
10.9
|
0.3
|
|
O
|
A:HOH635
|
3.3
|
10.5
|
0.2
|
|
O
|
A:HOH635
|
3.3
|
10.5
|
0.2
|
|
CB
|
A:LEU133
|
3.3
|
10.1
|
0.2
|
|
CB
|
A:LEU133
|
3.3
|
10.1
|
0.2
|
|
CD1
|
A:LEU133
|
3.3
|
10.4
|
0.2
|
|
CD1
|
A:LEU133
|
3.3
|
10.4
|
0.2
|
|
CA
|
A:SER38
|
3.4
|
8.9
|
0.3
|
|
CA
|
A:SER38
|
3.4
|
8.9
|
0.3
|
|
CA
|
A:SER38
|
3.4
|
9.3
|
0.2
|
|
CA
|
A:SER38
|
3.4
|
9.3
|
0.2
|
|
CB
|
A:LEU133
|
3.4
|
11.5
|
0.3
|
|
CB
|
A:LEU133
|
3.4
|
11.5
|
0.3
|
|
O
|
A:GLY37
|
3.5
|
9.6
|
0.3
|
|
O
|
A:GLY37
|
3.5
|
9.6
|
0.3
|
|
CG
|
A:LEU133
|
3.6
|
12.7
|
0.3
|
|
CG
|
A:LEU133
|
3.6
|
12.7
|
0.3
|
|
C7
|
A:RAY401
|
3.6
|
14.6
|
0.2
|
|
C7
|
A:RAY401
|
3.6
|
14.6
|
0.2
|
|
C5
|
A:RAY401
|
3.6
|
13.7
|
0.2
|
|
C5
|
A:RAY401
|
3.6
|
13.7
|
0.2
|
|
O
|
A:GLY37
|
3.6
|
9.7
|
0.2
|
|
O
|
A:GLY37
|
3.6
|
9.7
|
0.2
|
|
CB
|
A:SER38
|
3.7
|
9.4
|
0.3
|
|
CB
|
A:SER38
|
3.7
|
9.4
|
0.3
|
|
CB
|
A:SER38
|
3.8
|
9.6
|
0.2
|
|
CB
|
A:SER38
|
3.8
|
9.6
|
0.2
|
|
CG
|
A:LEU133
|
3.9
|
10.5
|
0.2
|
|
CG
|
A:LEU133
|
3.9
|
10.5
|
0.2
|
|
CD2
|
A:LEU133
|
3.9
|
13.6
|
0.3
|
|
CD2
|
A:LEU133
|
3.9
|
13.6
|
0.3
|
|
N
|
A:SER39
|
4.1
|
8.1
|
0.3
|
|
N
|
A:SER39
|
4.1
|
8.1
|
0.3
|
|
C6
|
A:RAY401
|
4.1
|
14.2
|
0.2
|
|
C6
|
A:RAY401
|
4.1
|
14.2
|
0.2
|
|
N
|
A:SER39
|
4.1
|
8.9
|
0.2
|
|
N
|
A:SER39
|
4.1
|
8.9
|
0.2
|
|
C
|
A:SER38
|
4.2
|
8.1
|
0.3
|
|
C
|
A:SER38
|
4.2
|
8.1
|
0.3
|
|
CE2
|
A:PHE194
|
4.2
|
13.6
|
0.2
|
|
CE2
|
A:PHE194
|
4.2
|
13.6
|
0.2
|
|
C
|
A:SER38
|
4.3
|
8.8
|
0.2
|
|
C
|
A:SER38
|
4.3
|
8.8
|
0.2
|
|
O
|
A:LEU133
|
4.3
|
10.9
|
0.3
|
|
O
|
A:LEU133
|
4.3
|
10.9
|
0.3
|
|
C
|
A:GLY37
|
4.3
|
8.6
|
0.3
|
|
C
|
A:GLY37
|
4.3
|
8.6
|
0.3
|
|
N
|
A:SER38
|
4.3
|
8.4
|
0.3
|
|
N
|
A:SER38
|
4.3
|
8.4
|
0.3
|
|
C
|
A:GLY37
|
4.3
|
9.1
|
0.2
|
|
C
|
A:GLY37
|
4.3
|
9.1
|
0.2
|
|
N
|
A:SER38
|
4.3
|
9.0
|
0.2
|
|
N
|
A:SER38
|
4.3
|
9.0
|
0.2
|
|
O
|
A:LEU133
|
4.4
|
11.5
|
0.2
|
|
O
|
A:LEU133
|
4.4
|
11.5
|
0.2
|
|
OG
|
A:SER39
|
4.5
|
8.7
|
0.3
|
|
OG
|
A:SER39
|
4.5
|
8.7
|
0.3
|
|
CE2
|
A:PHE194
|
4.5
|
11.5
|
0.3
|
|
CE2
|
A:PHE194
|
4.5
|
11.5
|
0.3
|
|
CZ
|
A:PHE194
|
4.5
|
13.4
|
0.2
|
|
CZ
|
A:PHE194
|
4.5
|
13.5
|
0.2
|
|
CA
|
A:LEU133
|
4.6
|
10.2
|
0.2
|
|
CA
|
A:LEU133
|
4.6
|
10.2
|
0.2
|
|
CD2
|
A:LEU133
|
4.7
|
10.2
|
0.2
|
|
CD2
|
A:LEU133
|
4.7
|
10.2
|
0.2
|
|
CA
|
A:LEU133
|
4.7
|
10.5
|
0.3
|
|
CA
|
A:LEU133
|
4.7
|
10.5
|
0.3
|
|
N
|
A:RAY401
|
4.7
|
13.9
|
0.2
|
|
N
|
A:RAY401
|
4.7
|
13.9
|
0.2
|
|
C
|
A:LEU133
|
4.8
|
10.1
|
0.2
|
|
C
|
A:LEU133
|
4.8
|
10.1
|
0.2
|
|
O
|
A:HOH541
|
4.8
|
16.0
|
0.2
|
|
O
|
A:HOH541
|
4.8
|
16.0
|
0.2
|
|
CD1
|
A:ILE77
|
4.8
|
12.6
|
0.2
|
|
CD1
|
A:ILE77
|
4.8
|
12.6
|
0.2
|
|
C
|
A:LEU133
|
4.8
|
9.8
|
0.3
|
|
C
|
A:LEU133
|
4.8
|
9.8
|
0.3
|
|
OG
|
A:SER39
|
4.9
|
9.0
|
0.2
|
|
OG
|
A:SER39
|
4.9
|
9.0
|
0.2
|
|
CB
|
A:SER39
|
4.9
|
8.9
|
0.3
|
|
CB
|
A:SER39
|
4.9
|
8.9
|
0.3
|
|
Reference:
J.Wollenhaupt,
A.Metz,
T.Barthel,
G.M.A.Lima,
A.Heine,
U.Mueller,
G.Klebe,
M.S.Weiss.
F2X-Universal and F2X-Entry: Structurally Diverse Compound Libraries For Crystallographic Fragment Screening. Structure 2020.
ISSN: ISSN 0969-2126
PubMed: 32413289
DOI: 10.1016/J.STR.2020.04.019
Page generated: Sun Dec 13 12:33:49 2020
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