Fluorine in PDB 6q0d: Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
Enzymatic activity of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
All present enzymatic activity of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution:
1.1.1.27;
Protein crystallography data
The structure of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution, PDB code: 6q0d
was solved by
D.M.Dranow,
D.R.Davies,
with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:
Resolution Low / High (Å)
|
46.68 /
2.05
|
Space group
|
C 1 2 1
|
Cell size a, b, c (Å), α, β, γ (°)
|
212.040,
128.070,
104.140,
90.00,
119.35,
90.00
|
R / Rfree (%)
|
18.4 /
22.5
|
Fluorine Binding Sites:
Pages:
>>> Page 1 <<<
Page 2, Binding sites: 11 -
12;
Binding sites:
The binding sites of Fluorine atom in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
(pdb code 6q0d). This binding sites where shown within
5.0 Angstroms radius around Fluorine atom.
In total 12 binding sites of Fluorine where determined in the
Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution, PDB code: 6q0d:
Jump to Fluorine binding site number:
1;
2;
3;
4;
5;
6;
7;
8;
9;
10;
Fluorine binding site 1 out
of 12 in 6q0d
Go back to
Fluorine Binding Sites List in 6q0d
Fluorine binding site 1 out
of 12 in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
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 Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F502
b:44.0
occ:1.00
|
F37
|
A:P8M502
|
0.0
|
44.0
|
1.0
|
C34
|
A:P8M502
|
1.4
|
45.0
|
1.0
|
C35
|
A:P8M502
|
2.4
|
43.9
|
1.0
|
C26
|
A:P8M502
|
2.4
|
37.5
|
1.0
|
C27
|
A:P8M502
|
2.8
|
43.2
|
1.0
|
CD2
|
A:LEU108
|
3.5
|
46.9
|
1.0
|
C28
|
A:P8M502
|
3.5
|
50.4
|
1.0
|
C36
|
A:P8M502
|
3.6
|
38.1
|
1.0
|
CG
|
A:LEU108
|
3.6
|
47.2
|
1.0
|
C25
|
A:P8M502
|
3.6
|
39.2
|
1.0
|
O
|
A:ARG105
|
3.7
|
40.9
|
1.0
|
CB
|
A:LEU108
|
3.8
|
45.6
|
1.0
|
CD
|
A:PRO138
|
4.1
|
26.8
|
1.0
|
C24
|
A:P8M502
|
4.1
|
34.3
|
1.0
|
N
|
A:VAL109
|
4.2
|
38.7
|
1.0
|
CB
|
A:ARG105
|
4.2
|
59.0
|
1.0
|
CA
|
A:ARG105
|
4.3
|
56.1
|
1.0
|
CD
|
A:ARG105
|
4.4
|
66.8
|
1.0
|
C
|
A:ARG105
|
4.4
|
48.6
|
1.0
|
C
|
A:LEU108
|
4.5
|
38.7
|
1.0
|
CA
|
A:VAL109
|
4.6
|
39.8
|
1.0
|
CG
|
A:ARG105
|
4.6
|
63.6
|
1.0
|
CB
|
A:VAL109
|
4.7
|
40.7
|
1.0
|
C29
|
A:P8M502
|
4.7
|
56.0
|
1.0
|
CA
|
A:LEU108
|
4.7
|
38.9
|
1.0
|
CG
|
A:PRO138
|
4.8
|
27.8
|
1.0
|
O
|
A:ASN137
|
4.8
|
29.2
|
1.0
|
N
|
A:PRO138
|
4.9
|
27.6
|
1.0
|
|
Fluorine binding site 2 out
of 12 in 6q0d
Go back to
Fluorine Binding Sites List in 6q0d
Fluorine binding site 2 out
of 12 in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
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 Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
A:F502
b:29.7
occ:1.00
|
F42
|
A:P8M502
|
0.0
|
29.7
|
1.0
|
C05
|
A:P8M502
|
1.3
|
30.3
|
1.0
|
C04
|
A:P8M502
|
2.3
|
30.1
|
1.0
|
C06
|
A:P8M502
|
2.4
|
34.2
|
1.0
|
O43
|
A:P8M502
|
2.9
|
35.9
|
1.0
|
S02
|
A:P8M502
|
2.9
|
32.6
|
1.0
|
N01
|
A:P8M502
|
3.2
|
36.6
|
1.0
|
N
|
A:VAL139
|
3.3
|
38.9
|
1.0
|
OD1
|
A:ASN137
|
3.4
|
30.5
|
1.0
|
O
|
A:HIS192
|
3.5
|
38.4
|
1.0
|
C09
|
A:P8M502
|
3.6
|
33.8
|
1.0
|
C07
|
A:P8M502
|
3.6
|
34.2
|
1.0
|
OD2
|
A:ASP140
|
3.6
|
36.4
|
1.0
|
CG1
|
A:VAL139
|
3.7
|
25.9
|
1.0
|
CB
|
A:HIS192
|
3.7
|
27.1
|
1.0
|
C
|
A:PRO138
|
3.8
|
31.6
|
1.0
|
CA
|
A:PRO138
|
3.9
|
29.2
|
1.0
|
N
|
A:ASP140
|
3.9
|
27.6
|
1.0
|
CD2
|
A:HIS192
|
4.1
|
29.5
|
1.0
|
C08
|
A:P8M502
|
4.1
|
34.0
|
1.0
|
CB
|
A:PRO138
|
4.1
|
28.1
|
1.0
|
C
|
A:HIS192
|
4.2
|
36.0
|
1.0
|
CG
|
A:HIS192
|
4.3
|
31.4
|
1.0
|
CA
|
A:VAL139
|
4.3
|
31.2
|
1.0
|
CA
|
A:HIS192
|
4.3
|
31.3
|
1.0
|
CG
|
A:ASP140
|
4.3
|
39.6
|
1.0
|
N
|
A:HIS192
|
4.3
|
25.3
|
1.0
|
O03
|
A:P8M502
|
4.4
|
33.5
|
1.0
|
CB
|
A:VAL139
|
4.5
|
25.8
|
1.0
|
CG
|
A:ASN137
|
4.6
|
36.0
|
1.0
|
C
|
A:VAL139
|
4.6
|
29.0
|
1.0
|
CB
|
A:ASP140
|
4.7
|
31.3
|
1.0
|
O
|
A:PRO138
|
4.8
|
32.5
|
1.0
|
C10
|
A:P8M502
|
4.9
|
32.0
|
1.0
|
CA
|
A:ASP140
|
4.9
|
32.0
|
1.0
|
|
Fluorine binding site 3 out
of 12 in 6q0d
Go back to
Fluorine Binding Sites List in 6q0d
Fluorine binding site 3 out
of 12 in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 3 of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F502
b:41.8
occ:1.00
|
F37
|
B:P8M502
|
0.0
|
41.8
|
1.0
|
C34
|
B:P8M502
|
1.4
|
38.1
|
1.0
|
C35
|
B:P8M502
|
2.3
|
35.8
|
1.0
|
C26
|
B:P8M502
|
2.4
|
32.9
|
1.0
|
C27
|
B:P8M502
|
2.8
|
35.1
|
1.0
|
CG
|
B:LEU108
|
3.2
|
32.0
|
1.0
|
CD2
|
B:LEU108
|
3.4
|
34.7
|
1.0
|
CB
|
B:LEU108
|
3.4
|
31.9
|
1.0
|
C28
|
B:P8M502
|
3.6
|
45.5
|
1.0
|
C36
|
B:P8M502
|
3.6
|
33.0
|
1.0
|
C25
|
B:P8M502
|
3.6
|
28.6
|
1.0
|
N
|
B:VAL109
|
3.8
|
32.8
|
1.0
|
CD
|
B:PRO138
|
3.8
|
34.5
|
1.0
|
O
|
B:ARG105
|
3.8
|
38.7
|
1.0
|
C
|
B:LEU108
|
4.0
|
28.9
|
1.0
|
C24
|
B:P8M502
|
4.1
|
29.4
|
1.0
|
CA
|
B:VAL109
|
4.2
|
33.5
|
1.0
|
CA
|
B:LEU108
|
4.3
|
29.3
|
1.0
|
CA
|
B:ARG105
|
4.4
|
36.8
|
1.0
|
CB
|
B:VAL109
|
4.4
|
33.8
|
1.0
|
CG
|
B:ARG105
|
4.4
|
49.0
|
1.0
|
CB
|
B:ARG105
|
4.4
|
41.4
|
1.0
|
O
|
B:ASN137
|
4.4
|
35.1
|
1.0
|
N
|
B:PRO138
|
4.6
|
38.8
|
1.0
|
ND2
|
B:ASN112
|
4.6
|
34.2
|
1.0
|
C
|
B:ARG105
|
4.6
|
37.5
|
1.0
|
O
|
B:LEU108
|
4.6
|
27.6
|
1.0
|
CD1
|
B:LEU108
|
4.6
|
33.0
|
1.0
|
CG
|
B:PRO138
|
4.7
|
29.6
|
1.0
|
C
|
B:ASN137
|
4.8
|
36.9
|
1.0
|
C29
|
B:P8M502
|
4.8
|
51.0
|
1.0
|
CD
|
B:ARG105
|
5.0
|
45.5
|
1.0
|
|
Fluorine binding site 4 out
of 12 in 6q0d
Go back to
Fluorine Binding Sites List in 6q0d
Fluorine binding site 4 out
of 12 in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 4 of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
B:F502
b:26.9
occ:1.00
|
F42
|
B:P8M502
|
0.0
|
26.9
|
1.0
|
C05
|
B:P8M502
|
1.3
|
30.2
|
1.0
|
C04
|
B:P8M502
|
2.3
|
27.5
|
1.0
|
C06
|
B:P8M502
|
2.4
|
25.9
|
1.0
|
S02
|
B:P8M502
|
3.0
|
28.1
|
1.0
|
O43
|
B:P8M502
|
3.0
|
25.4
|
1.0
|
N
|
B:VAL139
|
3.2
|
29.9
|
1.0
|
N01
|
B:P8M502
|
3.3
|
24.6
|
1.0
|
OD1
|
B:ASN137
|
3.4
|
30.3
|
1.0
|
CG1
|
B:VAL139
|
3.6
|
32.2
|
1.0
|
C09
|
B:P8M502
|
3.6
|
27.3
|
1.0
|
C07
|
B:P8M502
|
3.6
|
26.0
|
1.0
|
O
|
B:HIS192
|
3.7
|
30.8
|
1.0
|
CB
|
B:HIS192
|
3.7
|
27.3
|
1.0
|
OD2
|
B:ASP140
|
3.7
|
32.4
|
1.0
|
C
|
B:PRO138
|
3.8
|
33.7
|
1.0
|
CA
|
B:PRO138
|
3.8
|
28.1
|
1.0
|
N
|
B:ASP140
|
3.9
|
30.1
|
1.0
|
CD2
|
B:HIS192
|
4.0
|
30.1
|
1.0
|
CB
|
B:PRO138
|
4.0
|
28.9
|
1.0
|
C08
|
B:P8M502
|
4.1
|
24.5
|
1.0
|
CG
|
B:HIS192
|
4.2
|
30.3
|
1.0
|
CA
|
B:VAL139
|
4.2
|
26.8
|
1.0
|
CG
|
B:ASP140
|
4.3
|
32.0
|
1.0
|
C
|
B:HIS192
|
4.3
|
30.5
|
1.0
|
CA
|
B:HIS192
|
4.4
|
29.9
|
1.0
|
N
|
B:HIS192
|
4.4
|
30.9
|
1.0
|
CB
|
B:VAL139
|
4.4
|
29.2
|
1.0
|
O03
|
B:P8M502
|
4.5
|
32.3
|
1.0
|
CG
|
B:ASN137
|
4.5
|
32.1
|
1.0
|
C
|
B:VAL139
|
4.6
|
27.2
|
1.0
|
CB
|
B:ASP140
|
4.6
|
29.5
|
1.0
|
O
|
B:PRO138
|
4.7
|
30.7
|
1.0
|
C10
|
B:P8M502
|
4.9
|
25.1
|
1.0
|
CA
|
B:ASP140
|
4.9
|
29.6
|
1.0
|
|
Fluorine binding site 5 out
of 12 in 6q0d
Go back to
Fluorine Binding Sites List in 6q0d
Fluorine binding site 5 out
of 12 in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 5 of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F502
b:43.8
occ:1.00
|
F37
|
C:P8M502
|
0.0
|
43.8
|
1.0
|
C34
|
C:P8M502
|
1.4
|
37.6
|
1.0
|
C35
|
C:P8M502
|
2.4
|
37.2
|
1.0
|
C26
|
C:P8M502
|
2.4
|
30.6
|
1.0
|
C27
|
C:P8M502
|
2.7
|
37.0
|
1.0
|
C28
|
C:P8M502
|
3.5
|
46.7
|
1.0
|
C36
|
C:P8M502
|
3.6
|
30.4
|
1.0
|
C25
|
C:P8M502
|
3.6
|
34.5
|
1.0
|
O
|
C:ARG105
|
3.7
|
41.3
|
1.0
|
N
|
C:VAL109
|
3.7
|
50.4
|
1.0
|
CB
|
C:LEU108
|
3.8
|
40.3
|
1.0
|
CG
|
C:LEU108
|
3.8
|
47.9
|
1.0
|
CD
|
C:PRO138
|
3.8
|
50.3
|
1.0
|
CA
|
C:VAL109
|
3.9
|
50.5
|
1.0
|
CD2
|
C:LEU108
|
3.9
|
48.4
|
1.0
|
C
|
C:LEU108
|
4.0
|
47.6
|
1.0
|
C24
|
C:P8M502
|
4.1
|
34.8
|
1.0
|
ND2
|
C:ASN112
|
4.2
|
38.2
|
1.0
|
CA
|
C:ARG105
|
4.2
|
41.2
|
1.0
|
CB
|
C:VAL109
|
4.4
|
54.8
|
1.0
|
C
|
C:ARG105
|
4.4
|
47.2
|
1.0
|
O
|
C:ASN137
|
4.4
|
40.0
|
1.0
|
O
|
C:LEU108
|
4.4
|
40.0
|
1.0
|
CB
|
C:ARG105
|
4.4
|
41.6
|
1.0
|
CA
|
C:LEU108
|
4.5
|
45.8
|
1.0
|
N
|
C:PRO138
|
4.5
|
50.3
|
1.0
|
CG
|
C:ARG105
|
4.6
|
40.9
|
1.0
|
C29
|
C:P8M502
|
4.7
|
44.9
|
1.0
|
C
|
C:ASN137
|
4.7
|
45.7
|
1.0
|
CG
|
C:PRO138
|
4.8
|
46.8
|
1.0
|
|
Fluorine binding site 6 out
of 12 in 6q0d
Go back to
Fluorine Binding Sites List in 6q0d
Fluorine binding site 6 out
of 12 in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 6 of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
C:F502
b:40.5
occ:1.00
|
F42
|
C:P8M502
|
0.0
|
40.5
|
1.0
|
C05
|
C:P8M502
|
1.4
|
47.0
|
1.0
|
C04
|
C:P8M502
|
2.3
|
42.0
|
1.0
|
C06
|
C:P8M502
|
2.4
|
41.6
|
1.0
|
O43
|
C:P8M502
|
2.9
|
41.8
|
1.0
|
S02
|
C:P8M502
|
3.0
|
39.0
|
1.0
|
N
|
C:VAL139
|
3.2
|
38.6
|
1.0
|
N01
|
C:P8M502
|
3.3
|
37.6
|
1.0
|
OD1
|
C:ASN137
|
3.5
|
43.8
|
1.0
|
CG1
|
C:VAL139
|
3.5
|
42.5
|
1.0
|
C09
|
C:P8M502
|
3.6
|
38.8
|
1.0
|
C07
|
C:P8M502
|
3.6
|
44.6
|
1.0
|
O
|
C:HIS192
|
3.7
|
39.5
|
1.0
|
OD2
|
C:ASP140
|
3.8
|
39.4
|
1.0
|
CB
|
C:HIS192
|
3.8
|
46.2
|
1.0
|
C
|
C:PRO138
|
3.8
|
39.4
|
1.0
|
CA
|
C:PRO138
|
3.9
|
47.9
|
1.0
|
N
|
C:ASP140
|
3.9
|
39.0
|
1.0
|
CD2
|
C:HIS192
|
4.0
|
40.6
|
1.0
|
C08
|
C:P8M502
|
4.1
|
37.6
|
1.0
|
CA
|
C:VAL139
|
4.2
|
38.1
|
1.0
|
CB
|
C:PRO138
|
4.2
|
47.7
|
1.0
|
C
|
C:HIS192
|
4.3
|
50.6
|
1.0
|
CG
|
C:HIS192
|
4.3
|
39.9
|
1.0
|
CB
|
C:VAL139
|
4.3
|
41.5
|
1.0
|
CA
|
C:HIS192
|
4.4
|
48.1
|
1.0
|
O03
|
C:P8M502
|
4.4
|
39.9
|
1.0
|
CG
|
C:ASP140
|
4.5
|
42.9
|
1.0
|
N
|
C:HIS192
|
4.5
|
38.6
|
1.0
|
C
|
C:VAL139
|
4.6
|
38.5
|
1.0
|
CG
|
C:ASN137
|
4.6
|
47.9
|
1.0
|
CB
|
C:ASP140
|
4.7
|
41.3
|
1.0
|
O
|
C:PRO138
|
4.8
|
40.1
|
1.0
|
C10
|
C:P8M502
|
4.9
|
40.0
|
1.0
|
CA
|
C:ASP140
|
5.0
|
43.5
|
1.0
|
|
Fluorine binding site 7 out
of 12 in 6q0d
Go back to
Fluorine Binding Sites List in 6q0d
Fluorine binding site 7 out
of 12 in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 7 of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F502
b:50.6
occ:1.00
|
F37
|
D:P8M502
|
0.0
|
50.6
|
1.0
|
C34
|
D:P8M502
|
1.3
|
46.5
|
1.0
|
C26
|
D:P8M502
|
2.3
|
43.6
|
1.0
|
C35
|
D:P8M502
|
2.3
|
42.4
|
1.0
|
C27
|
D:P8M502
|
2.7
|
37.5
|
1.0
|
CD2
|
D:LEU108
|
3.4
|
73.4
|
1.0
|
C28
|
D:P8M502
|
3.5
|
46.0
|
1.0
|
C25
|
D:P8M502
|
3.6
|
41.7
|
1.0
|
C36
|
D:P8M502
|
3.6
|
38.2
|
1.0
|
O
|
D:ARG105
|
3.7
|
57.4
|
1.0
|
CG2
|
D:VAL109
|
3.7
|
54.2
|
1.0
|
CG
|
D:LEU108
|
3.8
|
70.4
|
1.0
|
CG
|
D:ARG105
|
3.9
|
81.9
|
1.0
|
C24
|
D:P8M502
|
4.1
|
36.5
|
1.0
|
CB
|
D:LEU108
|
4.1
|
67.7
|
1.0
|
CD
|
D:PRO138
|
4.1
|
40.8
|
1.0
|
CB
|
D:ARG105
|
4.2
|
76.3
|
1.0
|
CD
|
D:ARG105
|
4.3
|
85.8
|
1.0
|
CA
|
D:ARG105
|
4.4
|
71.8
|
1.0
|
C
|
D:ARG105
|
4.5
|
65.8
|
1.0
|
N
|
D:VAL109
|
4.5
|
57.5
|
1.0
|
NE
|
D:ARG105
|
4.6
|
86.6
|
1.0
|
O
|
D:ASN137
|
4.7
|
38.0
|
1.0
|
C29
|
D:P8M502
|
4.7
|
53.4
|
1.0
|
N
|
D:PRO138
|
4.9
|
40.4
|
1.0
|
C
|
D:LEU108
|
4.9
|
59.8
|
1.0
|
CG
|
D:PRO138
|
4.9
|
43.0
|
1.0
|
CA
|
D:VAL109
|
4.9
|
52.0
|
1.0
|
CB
|
D:VAL109
|
5.0
|
51.6
|
1.0
|
|
Fluorine binding site 8 out
of 12 in 6q0d
Go back to
Fluorine Binding Sites List in 6q0d
Fluorine binding site 8 out
of 12 in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 8 of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
D:F502
b:41.0
occ:1.00
|
F42
|
D:P8M502
|
0.0
|
41.0
|
1.0
|
C05
|
D:P8M502
|
1.4
|
42.4
|
1.0
|
C04
|
D:P8M502
|
2.3
|
40.9
|
1.0
|
C06
|
D:P8M502
|
2.4
|
45.8
|
1.0
|
O43
|
D:P8M502
|
2.8
|
33.8
|
1.0
|
S02
|
D:P8M502
|
2.9
|
37.7
|
1.0
|
N01
|
D:P8M502
|
3.2
|
33.1
|
1.0
|
N
|
D:VAL139
|
3.3
|
34.6
|
1.0
|
O
|
D:HIS192
|
3.6
|
38.1
|
1.0
|
OD1
|
D:ASN137
|
3.6
|
36.9
|
1.0
|
C09
|
D:P8M502
|
3.6
|
44.9
|
1.0
|
OD2
|
D:ASP140
|
3.6
|
34.2
|
1.0
|
C07
|
D:P8M502
|
3.6
|
44.1
|
1.0
|
CG1
|
D:VAL139
|
3.7
|
28.2
|
1.0
|
CB
|
D:HIS192
|
3.7
|
36.6
|
1.0
|
N
|
D:ASP140
|
3.8
|
31.8
|
1.0
|
C
|
D:PRO138
|
3.9
|
32.9
|
1.0
|
CA
|
D:PRO138
|
3.9
|
37.5
|
1.0
|
CD2
|
D:HIS192
|
4.1
|
39.9
|
1.0
|
C08
|
D:P8M502
|
4.1
|
44.3
|
1.0
|
CB
|
D:PRO138
|
4.1
|
39.4
|
1.0
|
CA
|
D:VAL139
|
4.3
|
28.9
|
1.0
|
N
|
D:HIS192
|
4.3
|
36.1
|
1.0
|
CG
|
D:HIS192
|
4.3
|
36.4
|
1.0
|
CG
|
D:ASP140
|
4.3
|
34.6
|
1.0
|
C
|
D:HIS192
|
4.3
|
37.5
|
1.0
|
CA
|
D:HIS192
|
4.3
|
36.6
|
1.0
|
O03
|
D:P8M502
|
4.4
|
39.8
|
1.0
|
CB
|
D:VAL139
|
4.5
|
29.4
|
1.0
|
CB
|
D:ASP140
|
4.5
|
31.6
|
1.0
|
C
|
D:VAL139
|
4.6
|
35.8
|
1.0
|
CG
|
D:ASN137
|
4.7
|
37.4
|
1.0
|
O
|
D:PRO138
|
4.8
|
39.9
|
1.0
|
CA
|
D:ASP140
|
4.8
|
33.7
|
1.0
|
C10
|
D:P8M502
|
4.9
|
34.2
|
1.0
|
|
Fluorine binding site 9 out
of 12 in 6q0d
Go back to
Fluorine Binding Sites List in 6q0d
Fluorine binding site 9 out
of 12 in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 9 of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F405
b:35.6
occ:1.00
|
F37
|
E:P8M405
|
0.0
|
35.6
|
1.0
|
C34
|
E:P8M405
|
1.3
|
33.5
|
1.0
|
C26
|
E:P8M405
|
2.3
|
27.6
|
1.0
|
C35
|
E:P8M405
|
2.4
|
34.3
|
1.0
|
C27
|
E:P8M405
|
2.7
|
29.9
|
1.0
|
C28
|
E:P8M405
|
3.5
|
28.9
|
1.0
|
CB
|
E:LEU108
|
3.5
|
33.2
|
1.0
|
C25
|
E:P8M405
|
3.6
|
26.6
|
1.0
|
C36
|
E:P8M405
|
3.6
|
29.4
|
1.0
|
CG
|
E:LEU108
|
3.7
|
41.2
|
1.0
|
CD2
|
E:LEU108
|
3.7
|
47.3
|
1.0
|
O
|
E:ARG105
|
3.8
|
28.2
|
1.0
|
N
|
E:VAL109
|
3.9
|
33.3
|
1.0
|
CD
|
E:PRO138
|
3.9
|
28.0
|
1.0
|
C
|
E:LEU108
|
4.1
|
35.6
|
1.0
|
CA
|
E:VAL109
|
4.1
|
33.4
|
1.0
|
C24
|
E:P8M405
|
4.1
|
29.7
|
1.0
|
CA
|
E:ARG105
|
4.2
|
38.3
|
1.0
|
ND2
|
E:ASN112
|
4.3
|
38.2
|
1.0
|
O
|
E:ASN137
|
4.4
|
28.0
|
1.0
|
CB
|
E:ARG105
|
4.4
|
36.9
|
1.0
|
CA
|
E:LEU108
|
4.4
|
33.7
|
1.0
|
C
|
E:ARG105
|
4.4
|
30.4
|
1.0
|
CB
|
E:VAL109
|
4.5
|
30.5
|
1.0
|
N
|
E:PRO138
|
4.6
|
26.5
|
1.0
|
CG
|
E:ARG105
|
4.6
|
37.6
|
1.0
|
O
|
E:LEU108
|
4.6
|
35.0
|
1.0
|
C29
|
E:P8M405
|
4.6
|
31.6
|
1.0
|
CG
|
E:PRO138
|
4.7
|
34.0
|
1.0
|
C
|
E:ASN137
|
4.7
|
26.0
|
1.0
|
O
|
E:HOH661
|
5.0
|
39.3
|
1.0
|
N
|
E:LEU108
|
5.0
|
33.5
|
1.0
|
|
Fluorine binding site 10 out
of 12 in 6q0d
Go back to
Fluorine Binding Sites List in 6q0d
Fluorine binding site 10 out
of 12 in the Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution
Mono view
Stereo pair view
|
A full contact list of Fluorine with other atoms in the F binding
site number 10 of Crystal Structure of Ldha in Complex with Compound NCGC00384414-01 at 2.05 A Resolution within 5.0Å range:
probe
|
atom
|
residue
|
distance (Å)
|
B
|
Occ
|
E:F405
b:26.7
occ:1.00
|
F42
|
E:P8M405
|
0.0
|
26.7
|
1.0
|
C05
|
E:P8M405
|
1.3
|
25.8
|
1.0
|
C04
|
E:P8M405
|
2.3
|
27.4
|
1.0
|
C06
|
E:P8M405
|
2.4
|
24.6
|
1.0
|
O43
|
E:P8M405
|
2.9
|
25.9
|
1.0
|
S02
|
E:P8M405
|
2.9
|
26.3
|
1.0
|
N01
|
E:P8M405
|
3.2
|
20.7
|
1.0
|
OD2
|
E:ASP140
|
3.4
|
21.4
|
1.0
|
N
|
E:VAL139
|
3.5
|
23.3
|
1.0
|
O
|
E:HIS192
|
3.5
|
22.1
|
1.0
|
CG1
|
E:VAL139
|
3.5
|
19.2
|
1.0
|
CB
|
E:HIS192
|
3.6
|
25.3
|
1.0
|
C09
|
E:P8M405
|
3.6
|
31.6
|
1.0
|
OD1
|
E:ASN137
|
3.6
|
24.2
|
1.0
|
C07
|
E:P8M405
|
3.6
|
29.5
|
1.0
|
N
|
E:ASP140
|
3.9
|
21.1
|
1.0
|
CD2
|
E:HIS192
|
3.9
|
27.7
|
1.0
|
C
|
E:PRO138
|
4.1
|
21.1
|
1.0
|
C08
|
E:P8M405
|
4.1
|
34.8
|
1.0
|
CA
|
E:PRO138
|
4.1
|
22.9
|
1.0
|
CG
|
E:HIS192
|
4.1
|
22.4
|
1.0
|
C
|
E:HIS192
|
4.1
|
24.4
|
1.0
|
CA
|
E:HIS192
|
4.2
|
27.1
|
1.0
|
N
|
E:HIS192
|
4.2
|
26.9
|
1.0
|
CG
|
E:ASP140
|
4.2
|
26.7
|
1.0
|
CB
|
E:PRO138
|
4.3
|
25.6
|
1.0
|
CA
|
E:VAL139
|
4.4
|
21.3
|
1.0
|
O03
|
E:P8M405
|
4.4
|
29.5
|
1.0
|
CB
|
E:VAL139
|
4.5
|
21.9
|
1.0
|
CB
|
E:ASP140
|
4.7
|
25.2
|
1.0
|
C
|
E:VAL139
|
4.7
|
24.0
|
1.0
|
CG
|
E:ASN137
|
4.8
|
31.3
|
1.0
|
C10
|
E:P8M405
|
4.9
|
26.0
|
1.0
|
CA
|
E:ASP140
|
5.0
|
25.9
|
1.0
|
O
|
E:PRO138
|
5.0
|
33.2
|
1.0
|
|
Reference:
G.Rai,
D.J.Urban,
B.T.Mott,
X.Hu,
S.M.Yang,
G.A.Benavides,
M.S.Johnson,
G.L.Squadrito,
K.R.Brimacombe,
T.D.Lee,
D.M.Cheff,
H.Zhu,
M.J.Henderson,
K.Pohida,
G.A.Sulikowski,
D.M.Dranow,
M.Kabir,
P.Shah,
E.Padilha,
D.Tao,
Y.Fang,
P.P.Christov,
K.Kim,
S.Jana,
P.Muttil,
T.Anderson,
N.K.Kunda,
H.J.Hathaway,
D.F.Kusewitt,
N.Oshima,
M.Cherukuri,
D.R.Davies,
J.P.Norenberg,
L.A.Sklar,
W.J.Moore,
C.V.Dang,
G.M.Stott,
L.Neckers,
A.J.Flint,
V.M.Darley-Usmar,
A.Simeonov,
A.G.Waterson,
A.Jadhav,
M.D.Hall,
D.J.Maloney.
Pyrazole-Based Lactate Dehydrogenase Inhibitors with Optimized Cell Activity and Pharmacokinetic Properties. J.Med.Chem. V. 63 10984 2020.
ISSN: ISSN 0022-2623
PubMed: 32902275
DOI: 10.1021/ACS.JMEDCHEM.0C00916
Page generated: Fri Aug 2 00:34:27 2024
|