Fluorine in PDB 6j3b: Crystal Structure of Human Dhodh in Complex with Inhibitor 1289

Enzymatic activity of Crystal Structure of Human Dhodh in Complex with Inhibitor 1289

All present enzymatic activity of Crystal Structure of Human Dhodh in Complex with Inhibitor 1289:
1.3.5.2;

Protein crystallography data

The structure of Crystal Structure of Human Dhodh in Complex with Inhibitor 1289, PDB code: 6j3b was solved by Y.Yu, Q.Chen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.39 / 1.60
Space group P 32 2 1
Cell size a, b, c (Å), α, β, γ (°) 90.829, 90.829, 122.754, 90.00, 90.00, 120.00
R / Rfree (%) 15.7 / 17.6

Other elements in 6j3b:

The structure of Crystal Structure of Human Dhodh in Complex with Inhibitor 1289 also contains other interesting chemical elements:

Chlorine (Cl) 3 atoms
Sodium (Na) 2 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1289 (pdb code 6j3b). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1289, PDB code: 6j3b:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 6j3b

Go back to Fluorine Binding Sites List in 6j3b
Fluorine binding site 1 out of 3 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1289


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 Human Dhodh in Complex with Inhibitor 1289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:33.2
occ:1.00
F17 A:B5O405 0.0 33.2 1.0
C15 A:B5O405 1.4 40.5 1.0
C14 A:B5O405 2.4 48.1 1.0
C16 A:B5O405 2.4 30.9 1.0
HG A:LEU359 2.4 21.9 0.6
H161 A:B5O405 2.7 37.1 1.0
F24 A:B5O405 2.7 32.1 1.0
C18 A:B5O405 2.9 34.0 1.0
HD3 A:PRO364 3.0 24.7 1.0
HB3 A:LEU359 3.0 19.4 0.5
C23 A:B5O405 3.0 30.6 1.0
HA2 A:GLY363 3.1 19.7 1.0
O A:LEU359 3.3 21.4 0.6
CG A:LEU359 3.4 18.3 0.6
O A:LEU359 3.6 17.2 0.5
C13 A:B5O405 3.6 47.7 1.0
C11 A:B5O405 3.7 39.8 1.0
HE1 A:MET43 3.8 34.4 1.0
HE2 A:MET43 3.9 34.4 1.0
HB1 A:ALA59 3.9 20.2 1.0
CD A:PRO364 3.9 20.6 1.0
CB A:LEU359 3.9 16.2 0.5
HD22 A:LEU359 4.0 32.9 0.5
HB3 A:LEU359 4.0 18.3 0.6
HG3 A:PRO364 4.0 24.6 1.0
C A:LEU359 4.0 20.7 0.6
CA A:GLY363 4.0 16.4 1.0
HD23 A:LEU359 4.0 24.1 0.6
C19 A:B5O405 4.1 36.6 1.0
HD21 A:LEU359 4.1 24.1 0.6
HD11 A:LEU359 4.1 13.9 0.6
C A:LEU359 4.1 20.8 0.5
HD12 A:LEU359 4.1 13.9 0.6
CD2 A:LEU359 4.1 20.1 0.6
C12 A:B5O405 4.2 41.4 1.0
CB A:LEU359 4.2 15.3 0.6
CD1 A:LEU359 4.2 11.6 0.6
C22 A:B5O405 4.2 37.2 1.0
CE A:MET43 4.3 28.6 1.0
HD13 A:LEU359 4.3 22.0 0.5
HB2 A:ALA59 4.3 20.2 1.0
HB2 A:LEU359 4.3 19.4 0.5
N A:PRO364 4.4 15.2 1.0
HA3 A:GLY363 4.4 19.7 1.0
HE1 A:PHE98 4.5 22.8 1.0
CA A:LEU359 4.5 17.4 0.5
CG A:PRO364 4.5 20.5 1.0
C A:GLY363 4.5 15.6 1.0
HA A:LEU359 4.5 20.8 0.5
HD2 A:PRO364 4.5 24.7 1.0
CA A:LEU359 4.5 18.3 0.6
H191 A:B5O405 4.5 43.9 1.0
HA A:THR360 4.6 27.8 1.0
HA A:LEU359 4.6 22.0 0.6
CB A:ALA59 4.6 16.9 1.0
H A:GLY363 4.7 18.7 1.0
CD2 A:LEU359 4.7 27.4 0.5
F27 A:B5O405 4.8 42.7 1.0
CG A:LEU359 4.8 4.6 0.5
H221 A:B5O405 4.8 44.6 1.0
N A:GLY363 4.9 15.6 1.0
N A:THR360 4.9 20.9 1.0
N8 A:B5O405 5.0 47.4 1.0
HG2 A:PRO364 5.0 24.6 1.0

Fluorine binding site 2 out of 3 in 6j3b

Go back to Fluorine Binding Sites List in 6j3b
Fluorine binding site 2 out of 3 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1289


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 Human Dhodh in Complex with Inhibitor 1289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:32.1
occ:1.00
F24 A:B5O405 0.0 32.1 1.0
C23 A:B5O405 1.4 30.6 1.0
C22 A:B5O405 2.4 37.2 1.0
C18 A:B5O405 2.4 34.0 1.0
HB1 A:ALA59 2.5 20.2 1.0
H221 A:B5O405 2.6 44.6 1.0
F17 A:B5O405 2.7 33.2 1.0
C14 A:B5O405 2.9 48.1 1.0
C15 A:B5O405 3.1 40.5 1.0
HZ A:PHE98 3.1 18.0 1.0
HG1 A:THR63 3.2 21.8 1.0
CB A:ALA59 3.4 16.9 1.0
OG1 A:THR63 3.5 18.1 1.0
HE1 A:MET111 3.6 24.1 1.0
HA A:ALA59 3.6 25.2 1.0
HB2 A:ALA59 3.7 20.2 1.0
C21 A:B5O405 3.7 38.4 1.0
C19 A:B5O405 3.7 36.6 1.0
HE1 A:PHE98 3.8 22.8 1.0
O A:ALA59 3.8 19.3 1.0
HG3 A:PRO364 3.8 24.6 1.0
CZ A:PHE98 3.8 15.0 1.0
CA A:ALA59 3.9 21.0 1.0
HG A:LEU359 3.9 21.9 0.6
HD21 A:LEU359 4.0 24.1 0.6
HB3 A:ALA59 4.1 20.2 1.0
C13 A:B5O405 4.1 47.7 1.0
C A:ALA59 4.1 17.3 1.0
CE1 A:PHE98 4.2 19.0 1.0
HD3 A:PRO364 4.2 24.7 1.0
C20 A:B5O405 4.2 44.2 1.0
HE2 A:MET111 4.2 24.1 1.0
C16 A:B5O405 4.3 30.9 1.0
CE A:MET111 4.3 20.1 1.0
HD23 A:LEU359 4.4 24.1 0.6
H211 A:B5O405 4.5 46.1 1.0
CD2 A:LEU359 4.6 20.1 0.6
H191 A:B5O405 4.6 43.9 1.0
CG A:PRO364 4.6 20.5 1.0
F27 A:B5O405 4.6 42.7 1.0
HD13 A:LEU359 4.7 22.0 0.5
CG A:LEU359 4.7 18.3 0.6
HB3 A:LEU359 4.8 19.4 0.5
HG2 A:PRO364 4.9 24.6 1.0
HD11 A:LEU359 4.9 13.9 0.6
CD A:PRO364 4.9 20.6 1.0
H161 A:B5O405 4.9 37.1 1.0
CB A:THR63 4.9 18.6 1.0
CE2 A:PHE98 4.9 15.1 1.0

Fluorine binding site 3 out of 3 in 6j3b

Go back to Fluorine Binding Sites List in 6j3b
Fluorine binding site 3 out of 3 in the Crystal Structure of Human Dhodh in Complex with Inhibitor 1289


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 Human Dhodh in Complex with Inhibitor 1289 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F405

b:42.7
occ:1.00
F27 A:B5O405 0.0 42.7 1.0
C13 A:B5O405 1.3 47.7 1.0
HD21 A:LEU46 2.3 66.7 0.5
C12 A:B5O405 2.4 41.4 1.0
C14 A:B5O405 2.4 48.1 1.0
H191 A:B5O405 2.6 43.9 1.0
H121 A:B5O405 2.6 49.7 1.0
C18 A:B5O405 2.8 34.0 1.0
C19 A:B5O405 2.9 36.6 1.0
HD13 A:LEU46 2.9 61.8 0.5
CD2 A:LEU46 3.0 55.6 0.5
HD23 A:LEU46 3.1 66.7 0.5
HA A:ALA59 3.1 25.2 1.0
HB2 A:ALA59 3.1 20.2 1.0
HD22 A:LEU46 3.2 66.7 0.5
CD1 A:LEU46 3.6 51.5 0.5
C15 A:B5O405 3.6 40.5 1.0
C11 A:B5O405 3.7 39.8 1.0
HD11 A:LEU46 3.7 61.8 0.5
CA A:ALA59 3.7 21.0 1.0
CB A:ALA59 3.8 16.9 1.0
HD12 A:LEU46 3.8 61.8 0.5
HD23 A:LEU58 3.9 50.0 1.0
C23 A:B5O405 4.0 30.6 1.0
HE1 A:MET43 4.0 34.4 1.0
N A:ALA59 4.0 20.6 1.0
H A:ALA59 4.0 24.8 1.0
C20 A:B5O405 4.1 44.2 1.0
HB1 A:ALA59 4.1 20.2 1.0
C16 A:B5O405 4.2 30.9 1.0
HB3 A:LEU58 4.2 28.1 1.0
O A:ALA55 4.3 20.2 1.0
CG A:LEU46 4.3 48.3 0.5
HG A:LEU58 4.3 51.4 1.0
HD11 A:LEU46 4.3 69.2 0.5
HG A:LEU46 4.5 57.9 0.5
H252 A:B5O405 4.5 60.3 1.0
C A:LEU58 4.6 21.9 1.0
F24 A:B5O405 4.6 32.1 1.0
HB3 A:ALA59 4.6 20.2 1.0
HB2 A:PHE62 4.8 32.9 1.0
CD2 A:LEU58 4.8 41.6 1.0
CD1 A:LEU46 4.8 57.7 0.5
F17 A:B5O405 4.8 33.2 1.0
HD22 A:LEU46 4.8 59.2 0.5
C25 A:B5O405 4.8 50.2 1.0
HB3 A:LEU46 4.9 51.0 0.5
N8 A:B5O405 4.9 47.4 1.0
CG A:LEU58 4.9 42.8 1.0
HD13 A:LEU46 4.9 69.2 0.5
C22 A:B5O405 4.9 37.2 1.0
C21 A:B5O405 4.9 38.4 1.0
CE A:MET43 4.9 28.6 1.0
CB A:LEU58 4.9 23.4 1.0
CG A:LEU46 4.9 51.2 0.5
O A:LEU58 5.0 22.4 1.0

Reference:

T.Zeng, Z.Zuo, Y.Luo, Y.Zhao, Y.Yu, Q.Chen. A Novel Series of Human Dihydroorotate Dehydrogenase Inhibitors Discovered By in Vitro Screening: Inhibition Activity and Crystallographic Binding Mode. Febs Open Bio V. 9 1348 2019.
ISSN: ESSN 2211-5463
PubMed: 31087527
DOI: 10.1002/2211-5463.12658
Page generated: Sun Dec 13 12:54:24 2020

Last articles

Zn in 8WB0
Zn in 8WAX
Zn in 8WAU
Zn in 8WAZ
Zn in 8WAY
Zn in 8WAV
Zn in 8WAW
Zn in 8WAT
Zn in 8W7M
Zn in 8WD3
© Copyright 2008-2020 by atomistry.com
Home   |    Site Map   |    Copyright   |    Contact us   |    Privacy