Atomistry » Fluorine » PDB 4ymq-4zg9 » 4ymq
Atomistry »
  Fluorine »
    PDB 4ymq-4zg9 »
      4ymq »

Fluorine in PDB 4ymq: X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist

Protein crystallography data

The structure of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist, PDB code: 4ymq was solved by X.Li, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 30.96 / 2.00
Space group P 41 21 2
Cell size a, b, c (Å), α, β, γ (°) 61.909, 61.909, 156.965, 90.00, 90.00, 90.00
R / Rfree (%) 19.8 / 23.9

Other elements in 4ymq:

The structure of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist also contains other interesting chemical elements:

Sodium (Na) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist (pdb code 4ymq). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist, PDB code: 4ymq:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 4ymq

Go back to Fluorine Binding Sites List in 4ymq
Fluorine binding site 1 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:67.8
occ:1.00
F20 A:ZBD603 0.0 67.8 1.0
C16 A:ZBD603 1.4 74.6 1.0
F21 A:ZBD603 2.3 63.0 1.0
F18 A:ZBD603 2.3 82.6 1.0
F19 A:ZBD603 2.3 79.4 1.0
C14 A:ZBD603 2.4 68.8 1.0
C15 A:ZBD603 2.6 66.7 1.0
F22 A:ZBD603 3.0 69.3 1.0
CD2 A:LEU396 3.3 36.7 1.0
C11 A:ZBD603 3.3 62.9 1.0
O17 A:ZBD603 3.5 68.6 1.0
C10 A:ZBD603 3.7 63.8 1.0
CD2 A:HIS479 3.8 42.4 1.0
F23 A:ZBD603 4.0 66.2 1.0
CG A:LEU396 4.3 32.1 1.0
C12 A:ZBD603 4.4 64.3 1.0
NE2 A:HIS479 4.5 44.0 1.0
SG A:CYS393 4.7 41.5 1.0
CG A:HIS479 4.7 33.9 1.0
CH2 A:TRP317 4.8 40.7 1.0
CD1 A:ILE397 4.8 44.1 1.0
CD1 A:ILE400 4.9 38.3 1.0
C9 A:ZBD603 5.0 64.6 1.0

Fluorine binding site 2 out of 6 in 4ymq

Go back to Fluorine Binding Sites List in 4ymq
Fluorine binding site 2 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:79.4
occ:1.00
F19 A:ZBD603 0.0 79.4 1.0
C16 A:ZBD603 1.4 74.6 1.0
F18 A:ZBD603 2.3 82.6 1.0
F20 A:ZBD603 2.3 67.8 1.0
C14 A:ZBD603 2.4 68.8 1.0
O17 A:ZBD603 2.5 68.6 1.0
F22 A:ZBD603 3.1 69.3 1.0
C15 A:ZBD603 3.3 66.7 1.0
C11 A:ZBD603 3.6 62.9 1.0
F21 A:ZBD603 3.8 63.0 1.0
CZ3 A:TRP317 4.0 36.8 1.0
CB A:CYS320 4.1 37.6 1.0
C12 A:ZBD603 4.1 64.3 1.0
CE3 A:TRP317 4.2 35.8 1.0
CH2 A:TRP317 4.4 40.7 1.0
CD2 A:HIS479 4.4 42.4 1.0
F23 A:ZBD603 4.5 66.2 1.0
NE2 A:HIS479 4.5 44.0 1.0
OH A:TYR502 4.6 39.3 1.0
C10 A:ZBD603 4.7 63.8 1.0
CD2 A:TRP317 4.8 33.1 1.0
CD1 A:LEU391 4.9 33.8 1.0
CZ2 A:TRP317 4.9 39.2 1.0

Fluorine binding site 3 out of 6 in 4ymq

Go back to Fluorine Binding Sites List in 4ymq
Fluorine binding site 3 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:82.6
occ:1.00
F18 A:ZBD603 0.0 82.6 1.0
C16 A:ZBD603 1.4 74.6 1.0
F19 A:ZBD603 2.3 79.4 1.0
F20 A:ZBD603 2.3 67.8 1.0
C14 A:ZBD603 2.4 68.8 1.0
C11 A:ZBD603 2.6 62.9 1.0
C12 A:ZBD603 3.0 64.3 1.0
O17 A:ZBD603 3.2 68.6 1.0
CD1 A:LEU391 3.3 33.8 1.0
C10 A:ZBD603 3.4 63.8 1.0
C15 A:ZBD603 3.7 66.7 1.0
CD1 A:ILE397 3.7 44.1 1.0
F21 A:ZBD603 3.8 63.0 1.0
C13 A:ZBD603 4.0 64.8 1.0
C9 A:ZBD603 4.3 64.6 1.0
F22 A:ZBD603 4.3 69.3 1.0
SG A:CYS393 4.3 41.5 1.0
CB A:CYS320 4.4 37.6 1.0
CG A:LEU391 4.5 32.7 1.0
C8 A:ZBD603 4.6 64.6 1.0
CD2 A:LEU391 4.6 28.9 1.0
SG A:CYS320 4.7 36.2 1.0
F23 A:ZBD603 4.7 66.2 1.0
CG1 A:ILE397 4.9 42.1 1.0
CD2 A:LEU396 4.9 36.7 1.0

Fluorine binding site 4 out of 6 in 4ymq

Go back to Fluorine Binding Sites List in 4ymq
Fluorine binding site 4 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:63.0
occ:1.00
F21 A:ZBD603 0.0 63.0 1.0
C15 A:ZBD603 1.4 66.7 1.0
F20 A:ZBD603 2.3 67.8 1.0
F22 A:ZBD603 2.3 69.3 1.0
F23 A:ZBD603 2.3 66.2 1.0
C14 A:ZBD603 2.4 68.8 1.0
C16 A:ZBD603 2.8 74.6 1.0
C10 A:ZBD603 2.9 63.8 1.0
C11 A:ZBD603 3.1 62.9 1.0
CD1 A:ILE400 3.4 38.3 1.0
O17 A:ZBD603 3.6 68.6 1.0
F18 A:ZBD603 3.8 82.6 1.0
F19 A:ZBD603 3.8 79.4 1.0
CD2 A:HIS479 3.9 42.4 1.0
CE A:MET358 3.9 42.0 1.0
CD2 A:LEU396 4.0 36.7 1.0
C9 A:ZBD603 4.2 64.6 1.0
CG A:HIS479 4.3 33.9 1.0
C12 A:ZBD603 4.4 64.3 1.0
CG A:LEU396 4.5 32.1 1.0
CB A:HIS479 4.5 32.4 1.0
NE2 A:HIS479 4.6 44.0 1.0
CD1 A:LEU396 4.8 35.5 1.0
CG1 A:ILE400 4.9 37.0 1.0

Fluorine binding site 5 out of 6 in 4ymq

Go back to Fluorine Binding Sites List in 4ymq
Fluorine binding site 5 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:69.3
occ:1.00
F22 A:ZBD603 0.0 69.3 1.0
C15 A:ZBD603 1.4 66.7 1.0
F23 A:ZBD603 2.3 66.2 1.0
F21 A:ZBD603 2.3 63.0 1.0
C14 A:ZBD603 2.4 68.8 1.0
O17 A:ZBD603 2.7 68.6 1.0
C16 A:ZBD603 3.0 74.6 1.0
F20 A:ZBD603 3.0 67.8 1.0
NE2 A:HIS479 3.1 44.0 1.0
CD2 A:HIS479 3.1 42.4 1.0
F19 A:ZBD603 3.1 79.4 1.0
CD2 A:LEU324 3.3 38.8 1.0
CE A:MET358 3.7 42.0 1.0
C11 A:ZBD603 3.7 62.9 1.0
CE1 A:HIS479 3.8 40.0 1.0
CG A:HIS479 3.8 33.9 1.0
ND1 A:HIS479 4.2 39.1 1.0
C10 A:ZBD603 4.3 63.8 1.0
F18 A:ZBD603 4.3 82.6 1.0
CG A:LEU324 4.4 41.2 1.0
CD1 A:LEU324 4.6 38.1 1.0
CB A:LEU324 4.7 31.9 1.0
C12 A:ZBD603 4.8 64.3 1.0
SD A:MET358 4.8 41.1 1.0
CB A:HIS479 4.8 32.4 1.0
OH A:TYR502 4.9 39.3 1.0

Fluorine binding site 6 out of 6 in 4ymq

Go back to Fluorine Binding Sites List in 4ymq
Fluorine binding site 6 out of 6 in the X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of X-Ray Co-Structure of Nuclear Receptor Ror-Gammat + SRC2 Peptide with A Benzothiadiazole Dioxide Inverse Agonist within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F603

b:66.2
occ:1.00
F23 A:ZBD603 0.0 66.2 1.0
C15 A:ZBD603 1.4 66.7 1.0
F22 A:ZBD603 2.3 69.3 1.0
F21 A:ZBD603 2.3 63.0 1.0
C14 A:ZBD603 2.4 68.8 1.0
C11 A:ZBD603 2.8 62.9 1.0
O17 A:ZBD603 2.9 68.6 1.0
C10 A:ZBD603 3.0 63.8 1.0
CE A:MET358 3.5 42.0 1.0
C16 A:ZBD603 3.8 74.6 1.0
C12 A:ZBD603 3.9 64.3 1.0
F20 A:ZBD603 4.0 67.8 1.0
CD1 A:LEU324 4.0 38.1 1.0
C9 A:ZBD603 4.1 64.6 1.0
CD2 A:LEU324 4.1 38.8 1.0
CD1 A:ILE400 4.5 38.3 1.0
F19 A:ZBD603 4.5 79.4 1.0
CG A:LEU324 4.6 41.2 1.0
CE A:MET365 4.6 62.4 1.0
SD A:MET358 4.7 41.1 1.0
F18 A:ZBD603 4.7 82.6 1.0
C13 A:ZBD603 4.8 64.8 1.0
CB A:LEU324 4.9 31.9 1.0
C8 A:ZBD603 4.9 64.6 1.0
SD A:MET365 4.9 55.2 1.0

Reference:

I.Muegge, D.Collin, B.Cook, M.Hill-Drzewi, J.Horan, S.Kugler, M.Labadia, X.Li, L.Smith, Y.Zhang. Discovery of 1,3-Dihydro-2,1,3-Benzothiadiazole 2,2-Dioxide Analogs As New Rorc Modulators. Bioorg.Med.Chem.Lett. V. 25 1892 2015.
ISSN: ESSN 1464-3405
PubMed: 25840886
DOI: 10.1016/J.BMCL.2015.03.042
Page generated: Sun Dec 13 12:16:08 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