Fluorine in PDB 6zbv: Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7

Protein crystallography data

The structure of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7, PDB code: 6zbv was solved by A.Shahsavar, P.Stohler, G.Bourenkov, I.Zimmermann, M.Siegrist, W.Guba, E.Pinard, S.Sinning, M.A.Seeger, T.R.Schneider, R.J.P.Dawson, P.Nissen, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.67 / 3.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 65.17, 58.14, 122.31, 90, 100.38, 90
R / Rfree (%) 21.4 / 25.9

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7 (pdb code 6zbv). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7, PDB code: 6zbv:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 6zbv

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Fluorine binding site 1 out of 6 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:118.9
occ:1.00
F01 A:QET701 0.0 118.9 1.0
C07 A:QET701 1.4 118.7 1.0
F02 A:QET701 2.2 119.0 1.0
C06 A:QET701 2.4 118.3 1.0
C08 A:QET701 2.4 118.7 1.0
H08 A:QET701 2.5 142.0 1.0
HA3 A:GLY378 2.5 122.8 1.0
H16 A:QET701 2.7 142.0 1.0
F03 A:QET701 2.7 118.7 1.0
F05 A:QET701 2.8 118.7 1.0
H A:LEU379 3.0 123.0 1.0
N A:LEU379 3.1 102.5 1.0
C A:GLY378 3.1 102.6 1.0
CA A:GLY378 3.2 102.3 1.0
HG A:LEU379 3.2 126.5 1.0
HD21 A:LEU379 3.2 127.6 1.0
O03 A:QET701 3.5 118.0 1.0
F04 A:QET701 3.6 118.5 1.0
HA A:LEU379 3.6 123.6 1.0
H A:GLY378 3.7 122.0 1.0
O A:GLY378 3.8 102.7 1.0
N A:GLY378 3.9 101.7 1.0
CA A:LEU379 3.9 103.0 1.0
HA3 A:GLY373 3.9 123.5 1.0
HB2 A:TRP376 3.9 121.3 1.0
CD2 A:LEU379 4.0 106.3 1.0
CG A:LEU379 4.0 105.4 1.0
HA2 A:GLY378 4.1 122.8 1.0
HD22 A:LEU379 4.2 127.6 1.0
H09 A:QET701 4.3 141.1 1.0
O A:GLY373 4.3 103.2 1.0
CB A:LEU379 4.5 103.5 1.0
HG3 A:MET382 4.5 124.8 1.0
CA A:GLY373 4.7 102.9 1.0
C05 A:QET701 4.8 117.7 1.0
HA2 A:GLY373 4.8 123.5 1.0
HE3 A:TRP376 4.9 121.4 1.0
CB A:TRP376 4.9 101.1 1.0
HB2 A:LEU379 4.9 124.2 1.0
HD23 A:LEU379 4.9 127.6 1.0
SD A:MET382 5.0 110.0 1.0
HB3 A:CYS475 5.0 123.8 1.0
C A:GLY373 5.0 103.2 1.0
H02 A:QET701 5.0 140.9 1.0
HB3 A:TRP376 5.0 121.3 1.0
C11 A:QET701 5.0 117.5 1.0

Fluorine binding site 2 out of 6 in 6zbv

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Fluorine binding site 2 out of 6 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:119.0
occ:1.00
F02 A:QET701 0.0 119.0 1.0
C07 A:QET701 1.4 118.7 1.0
F01 A:QET701 2.2 118.9 1.0
C08 A:QET701 2.3 118.7 1.0
C06 A:QET701 2.4 118.3 1.0
H08 A:QET701 2.6 142.0 1.0
O03 A:QET701 2.6 118.0 1.0
F03 A:QET701 2.6 118.7 1.0
F04 A:QET701 2.8 118.5 1.0
H18 A:QET701 3.0 141.3 1.0
H09 A:QET701 3.1 141.1 1.0
H16 A:QET701 3.2 142.0 1.0
HB3 A:CYS475 3.4 123.8 1.0
N01 A:QET701 3.4 117.5 1.0
C11 A:QET701 3.5 117.5 1.0
C18 A:QET701 3.5 117.8 1.0
F05 A:QET701 3.5 118.7 1.0
C17 A:QET701 3.6 117.9 1.0
C12 A:QET701 3.7 117.7 1.0
HD21 A:LEU379 3.8 127.6 1.0
SD A:MET382 3.9 110.0 1.0
HB2 A:CYS475 3.9 123.8 1.0
C05 A:QET701 4.0 117.7 1.0
C10 A:QET701 4.0 117.4 1.0
HA3 A:GLY378 4.1 122.8 1.0
CB A:CYS475 4.1 103.1 1.0
H17 A:QET701 4.4 141.1 1.0
H10 A:QET701 4.4 141.3 1.0
HG3 A:MET382 4.5 124.8 1.0
O04 A:QET701 4.5 117.4 1.0
C16 A:QET701 4.5 118.2 1.0
C09 A:QET701 4.5 117.5 1.0
HA A:LEU379 4.7 123.6 1.0
C A:GLY378 4.7 102.6 1.0
C13 A:QET701 4.7 117.9 1.0
CD2 A:LEU379 4.7 106.3 1.0
HD22 A:LEU379 4.7 127.6 1.0
HA3 A:GLY373 4.7 123.5 1.0
HG A:LEU379 4.8 126.5 1.0
H04 A:QET701 4.8 141.8 1.0
N A:LEU379 4.9 102.5 1.0
CG A:MET382 4.9 104.0 1.0
O A:GLY378 4.9 102.7 1.0
CA A:GLY378 4.9 102.3 1.0
HG23 A:THR472 4.9 115.9 1.0

Fluorine binding site 3 out of 6 in 6zbv

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Fluorine binding site 3 out of 6 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:118.7
occ:1.00
F03 A:QET701 0.0 118.7 1.0
C08 A:QET701 1.4 118.7 1.0
F04 A:QET701 2.2 118.5 1.0
F05 A:QET701 2.2 118.7 1.0
C07 A:QET701 2.3 118.7 1.0
HA3 A:GLY378 2.6 122.8 1.0
F02 A:QET701 2.6 119.0 1.0
F01 A:QET701 2.7 118.9 1.0
O A:CYS475 2.9 102.5 1.0
HA A:LEU476 3.0 123.2 1.0
HG1 A:THR479 3.1 124.7 1.0
HB3 A:CYS475 3.1 123.8 1.0
C A:CYS475 3.3 102.3 1.0
OG1 A:THR479 3.5 103.9 1.0
N A:LEU476 3.6 102.1 1.0
HB2 A:CYS475 3.6 123.8 1.0
CA A:GLY378 3.7 102.3 1.0
C06 A:QET701 3.7 118.3 1.0
CB A:CYS475 3.7 103.1 1.0
CA A:LEU476 3.7 102.7 1.0
H16 A:QET701 4.0 142.0 1.0
HA2 A:GLY378 4.0 122.8 1.0
HB A:THR479 4.1 124.0 1.0
CA A:CYS475 4.1 102.4 1.0
HG3 A:MET382 4.1 124.8 1.0
O03 A:QET701 4.1 118.0 1.0
HB2 A:LEU476 4.2 123.7 1.0
C A:GLY378 4.2 102.6 1.0
H A:LEU476 4.2 122.5 1.0
CB A:THR479 4.3 103.3 1.0
H08 A:QET701 4.4 142.0 1.0
HG21 A:THR479 4.5 124.5 1.0
HE3 A:TRP376 4.5 121.4 1.0
H A:GLY378 4.5 122.0 1.0
O A:GLY378 4.5 102.7 1.0
SD A:MET382 4.6 110.0 1.0
HA A:CYS475 4.6 122.8 1.0
CB A:LEU476 4.6 103.1 1.0
N A:GLY378 4.7 101.7 1.0
HD13 A:LEU476 4.7 126.7 1.0
H A:THR479 4.8 123.7 1.0
C A:LEU476 4.9 103.0 1.0
HD11 A:LEU476 4.9 126.7 1.0
H18 A:QET701 4.9 141.3 1.0
CG A:MET382 4.9 104.0 1.0
N A:LEU379 5.0 102.5 1.0
CG2 A:THR479 5.0 103.7 1.0

Fluorine binding site 4 out of 6 in 6zbv

Go back to Fluorine Binding Sites List in 6zbv
Fluorine binding site 4 out of 6 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:118.5
occ:1.00
F04 A:QET701 0.0 118.5 1.0
C08 A:QET701 1.4 118.7 1.0
F03 A:QET701 2.2 118.7 1.0
F05 A:QET701 2.2 118.7 1.0
C07 A:QET701 2.4 118.7 1.0
O03 A:QET701 2.7 118.0 1.0
F02 A:QET701 2.8 119.0 1.0
HG23 A:THR472 2.9 115.9 1.0
HB2 A:CYS475 2.9 123.8 1.0
C06 A:QET701 3.0 118.3 1.0
H16 A:QET701 3.1 142.0 1.0
HB2 A:LEU476 3.2 123.7 1.0
HA A:LEU476 3.5 123.2 1.0
HB3 A:CYS475 3.5 123.8 1.0
N A:LEU476 3.6 102.1 1.0
F01 A:QET701 3.6 118.9 1.0
HZ3 A:TRP376 3.6 122.4 1.0
O A:THR472 3.6 97.2 1.0
CB A:CYS475 3.7 103.1 1.0
H A:LEU476 3.7 122.5 1.0
HE3 A:TRP376 3.7 121.4 1.0
C A:CYS475 3.8 102.3 1.0
H08 A:QET701 3.8 142.0 1.0
CA A:LEU476 3.9 102.7 1.0
CG2 A:THR472 3.9 96.6 1.0
C05 A:QET701 3.9 117.7 1.0
CZ3 A:TRP376 4.0 102.0 1.0
CE3 A:TRP376 4.0 101.2 1.0
CB A:LEU476 4.0 103.1 1.0
HA A:THR472 4.0 115.5 1.0
HG22 A:THR472 4.1 115.9 1.0
O A:CYS475 4.1 102.5 1.0
CA A:CYS475 4.3 102.4 1.0
H18 A:QET701 4.3 141.3 1.0
C10 A:QET701 4.3 117.4 1.0
O04 A:QET701 4.3 117.4 1.0
HG21 A:THR472 4.4 115.9 1.0
HD13 A:LEU476 4.4 126.7 1.0
HA3 A:GLY378 4.4 122.8 1.0
C A:THR472 4.6 97.3 1.0
C09 A:QET701 4.6 117.5 1.0
HB3 A:LEU476 4.6 123.7 1.0
N01 A:QET701 4.6 117.5 1.0
HG1 A:THR472 4.7 117.5 1.0
CA A:THR472 4.7 96.2 1.0
H02 A:QET701 4.7 140.9 1.0
C04 A:QET701 4.7 117.4 1.0
CB A:THR472 4.8 96.8 1.0
H09 A:QET701 4.8 141.1 1.0
H A:CYS475 4.9 122.6 1.0
C18 A:QET701 5.0 117.8 1.0
CH2 A:TRP376 5.0 102.2 1.0
HG1 A:THR479 5.0 124.7 1.0

Fluorine binding site 5 out of 6 in 6zbv

Go back to Fluorine Binding Sites List in 6zbv
Fluorine binding site 5 out of 6 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 5 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:118.7
occ:1.00
F05 A:QET701 0.0 118.7 1.0
C08 A:QET701 1.4 118.7 1.0
F04 A:QET701 2.2 118.5 1.0
F03 A:QET701 2.2 118.7 1.0
HE3 A:TRP376 2.4 121.4 1.0
C07 A:QET701 2.4 118.7 1.0
H16 A:QET701 2.6 142.0 1.0
F01 A:QET701 2.8 118.9 1.0
C06 A:QET701 3.0 118.3 1.0
CE3 A:TRP376 3.0 101.2 1.0
HA3 A:GLY378 3.0 122.8 1.0
HA A:LEU476 3.2 123.2 1.0
HD13 A:LEU476 3.3 126.7 1.0
HB2 A:TRP376 3.3 121.3 1.0
HB3 A:TRP376 3.4 121.3 1.0
F02 A:QET701 3.5 119.0 1.0
HB2 A:LEU476 3.6 123.7 1.0
O03 A:QET701 3.6 118.0 1.0
H A:GLY378 3.7 122.0 1.0
H08 A:QET701 3.8 142.0 1.0
CZ3 A:TRP376 3.8 102.0 1.0
CD2 A:TRP376 3.8 100.7 1.0
HZ3 A:TRP376 3.8 122.4 1.0
CB A:TRP376 3.8 101.1 1.0
CA A:GLY378 4.0 102.3 1.0
CA A:LEU476 4.1 102.7 1.0
CG A:TRP376 4.2 100.8 1.0
CD1 A:LEU476 4.2 105.6 1.0
HD11 A:LEU476 4.2 126.7 1.0
CB A:LEU476 4.3 103.1 1.0
N A:GLY378 4.3 101.7 1.0
N A:LEU476 4.5 102.1 1.0
HG23 A:THR472 4.5 115.9 1.0
O A:CYS475 4.7 102.5 1.0
H02 A:QET701 4.7 140.9 1.0
HA2 A:GLY378 4.7 122.8 1.0
HG21 A:THR479 4.8 124.5 1.0
C A:CYS475 4.8 102.3 1.0
C05 A:QET701 4.8 117.7 1.0
HG1 A:THR479 4.8 124.7 1.0
HD22 A:LEU476 4.8 126.9 1.0
CG A:LEU476 4.8 104.9 1.0
O A:TRP376 4.9 102.1 1.0
C A:GLY378 4.9 102.6 1.0
HB A:THR479 4.9 124.0 1.0
H A:LEU379 4.9 123.0 1.0
CH2 A:TRP376 4.9 102.2 1.0
CE2 A:TRP376 4.9 101.2 1.0
HB2 A:CYS475 4.9 123.8 1.0
H A:LEU476 4.9 122.5 1.0

Fluorine binding site 6 out of 6 in 6zbv

Go back to Fluorine Binding Sites List in 6zbv
Fluorine binding site 6 out of 6 in the Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 6 of Inward-Open Structure of Human Glycine Transporter 1 in Complex with A Benzoylisoindoline Inhibitor and Sybody SB_GLYT1#7 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F701

b:117.8
occ:1.00
F06 A:QET701 0.0 117.8 1.0
C14 A:QET701 1.3 118.1 1.0
C15 A:QET701 2.3 118.5 1.0
C13 A:QET701 2.3 117.9 1.0
H06 A:QET701 2.4 143.6 1.0
H13 A:QET701 2.4 143.8 1.0
H03 A:QET701 2.4 141.4 1.0
HD13 A:ILE399 2.7 125.5 1.0
C22 A:QET701 2.8 119.7 1.0
O05 A:QET701 2.9 119.3 1.0
C23 A:QET701 3.0 119.8 1.0
HD21 A:LEU158 3.2 123.0 1.0
HD12 A:ILE399 3.2 125.5 1.0
CD1 A:ILE399 3.3 104.5 1.0
HZ A:PHE154 3.5 114.0 1.0
C16 A:QET701 3.5 118.2 1.0
HD11 A:ILE399 3.6 125.5 1.0
H21 A:QET701 3.7 143.8 1.0
C12 A:QET701 3.8 117.7 1.0
HE1 A:PHE154 3.8 114.3 1.0
HD23 A:LEU379 3.8 127.6 1.0
H22 A:QET701 3.8 144.1 1.0
HD13 A:LEU158 4.0 123.1 1.0
C24 A:QET701 4.0 120.1 1.0
HD2 A:TYR116 4.0 124.9 1.0
HG21 A:ILE399 4.1 122.4 1.0
H04 A:QET701 4.1 141.8 1.0
CD2 A:LEU158 4.2 102.5 1.0
C17 A:QET701 4.2 117.9 1.0
HD23 A:LEU158 4.2 123.0 1.0
CZ A:PHE154 4.3 95.0 1.0
C21 A:QET701 4.3 119.9 1.0
HD21 A:LEU379 4.3 127.6 1.0
CE1 A:PHE154 4.4 95.2 1.0
CD2 A:LEU379 4.4 106.3 1.0
HD22 A:LEU379 4.5 127.6 1.0
CD2 A:TYR116 4.5 104.1 1.0
H20 A:QET701 4.6 143.9 1.0
HB3 A:TYR116 4.6 123.2 1.0
H14 A:QET701 4.6 144.1 1.0
HD12 A:LEU158 4.7 123.1 1.0
CG1 A:ILE399 4.8 103.0 1.0
CD1 A:LEU158 4.8 102.6 1.0
HD22 A:LEU158 4.8 123.0 1.0
H12 A:QET701 4.8 143.9 1.0
H19 A:QET701 4.9 144.2 1.0
HE2 A:TYR116 4.9 125.8 1.0
CE2 A:TYR116 5.0 104.8 1.0
C20 A:QET701 5.0 120.2 1.0

Reference:

A.Shahsavar, P.Stohler, G.Bourenkov, I.Zimmermann, M.Siegrist, W.Guba, E.Pinard, S.Sinning, M.A.Seeger, T.R.Schneider, R.J.P.Dawson, P.Nissen. Structural Insights Into the Inhibition of Glycine Reuptake. Nature 2021.
ISSN: ESSN 1476-4687
PubMed: 33658720
DOI: 10.1038/S41586-021-03274-Z
Page generated: Sat Apr 3 15:05:13 2021

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