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Fluorine in PDB 7u9s: Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor

Enzymatic activity of Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor

All present enzymatic activity of Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor:
1.4.3.3;

Protein crystallography data

The structure of Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor, PDB code: 7u9s was solved by R.J.Skene, J.A.Bell, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 48.82 / 2.10
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 123.091, 73.155, 80.19, 90, 90, 90
R / Rfree (%) 25.7 / 29.3

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor (pdb code 7u9s). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 6 binding sites of Fluorine where determined in the Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor, PDB code: 7u9s:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6;

Fluorine binding site 1 out of 6 in 7u9s

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Fluorine binding site 1 out of 6 in the Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor


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 D-Amino Acid Oxidase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:43.1
occ:1.00
F1 A:M7I402 0.0 43.1 1.0
C11 A:M7I402 1.3 34.4 1.0
F2 A:M7I402 2.2 47.1 1.0
F3 A:M7I402 2.2 42.7 1.0
H1 A:HOH563 2.3 27.0 1.0
C8 A:M7I402 2.4 42.4 1.0
H9 A:M7I402 2.4 32.8 1.0
HG22 A:ILE223 2.5 58.8 1.0
C9 A:M7I402 2.7 30.8 1.0
HE1 A:HIS217 2.9 37.3 1.0
HB A:ILE223 3.0 59.3 1.0
HA A:ILE223 3.1 53.4 1.0
CG2 A:ILE223 3.2 56.8 1.0
O A:HOH563 3.3 25.0 1.0
HD11 A:LEU56 3.4 45.3 1.0
HG21 A:ILE223 3.4 58.8 1.0
HG A:LEU56 3.5 56.7 1.0
ND1 A:HIS217 3.5 38.1 1.0
CE1 A:HIS217 3.5 35.3 1.0
CB A:ILE223 3.5 57.3 1.0
H A:TYR224 3.5 44.1 1.0
HD12 A:LEU56 3.5 45.3 1.0
C7 A:M7I402 3.7 42.1 1.0
H2 A:HOH563 3.7 27.0 1.0
CA A:ILE223 3.8 51.4 1.0
CD1 A:LEU56 3.9 43.3 1.0
H7 A:M7I402 4.0 44.1 1.0
C10 A:M7I402 4.1 33.2 1.0
HG23 A:ILE223 4.2 58.8 1.0
CG A:LEU56 4.2 54.7 1.0
N A:TYR224 4.2 42.1 1.0
HE1 A:TYR224 4.3 45.7 1.0
CE1 A:TYR224 4.3 43.7 1.0
HA A:TYR55 4.4 44.7 1.0
H2 A:HOH510 4.5 30.5 1.0
CD1 A:TYR224 4.5 47.8 1.0
H A:LEU56 4.5 60.8 1.0
C A:ILE223 4.5 45.0 1.0
HD1 A:TYR224 4.6 49.8 1.0
HD21 A:LEU56 4.7 60.4 1.0
NE2 A:HIS217 4.7 34.0 1.0
HE21 A:GLN53 4.7 32.5 1.0
H10 A:M7I402 4.8 35.2 1.0
CZ A:TYR224 4.8 38.0 1.0
C6 A:M7I402 4.8 37.2 1.0
CG A:HIS217 4.8 38.1 1.0
HD13 A:LEU56 4.9 45.3 1.0
N A:ILE223 5.0 57.0 1.0
CG1 A:ILE223 5.0 66.1 1.0
C5 A:M7I402 5.0 34.4 1.0

Fluorine binding site 2 out of 6 in 7u9s

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Fluorine binding site 2 out of 6 in the Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor


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 D-Amino Acid Oxidase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:47.1
occ:1.00
F2 A:M7I402 0.0 47.1 1.0
C11 A:M7I402 1.3 34.4 1.0
F3 A:M7I402 2.2 42.7 1.0
F1 A:M7I402 2.2 43.1 1.0
C8 A:M7I402 2.4 42.4 1.0
HA A:TYR55 2.5 44.7 1.0
H7 A:M7I402 2.7 44.1 1.0
C7 A:M7I402 2.9 42.1 1.0
HG21 A:ILE223 3.1 58.8 1.0
HG22 A:ILE223 3.3 58.8 1.0
HG A:LEU56 3.3 56.7 1.0
HD1 A:TYR55 3.4 59.1 1.0
HB A:ILE223 3.4 59.3 1.0
C9 A:M7I402 3.5 30.8 1.0
H A:LEU56 3.5 60.8 1.0
O A:PRO54 3.6 27.4 1.0
CA A:TYR55 3.6 42.7 1.0
CG2 A:ILE223 3.6 56.8 1.0
HH A:TYR224 3.8 64.5 1.0
H9 A:M7I402 3.8 32.8 1.0
HE1 A:TYR224 3.8 45.7 1.0
OH A:TYR224 3.9 62.5 1.0
HE21 A:GLN53 4.0 32.5 1.0
CE1 A:TYR224 4.0 43.7 1.0
N A:LEU56 4.0 58.8 1.0
CZ A:TYR224 4.1 38.0 1.0
CB A:ILE223 4.1 57.3 1.0
HE1 A:HIS217 4.2 37.3 1.0
CD1 A:TYR55 4.2 57.1 1.0
C A:TYR55 4.2 42.9 1.0
C6 A:M7I402 4.2 37.2 1.0
C A:PRO54 4.3 43.2 1.0
N A:TYR55 4.3 45.1 1.0
HD12 A:ILE223 4.3 59.2 1.0
CG A:LEU56 4.4 54.7 1.0
HB3 A:TYR55 4.4 32.2 1.0
H1 A:HOH563 4.4 27.0 1.0
CB A:TYR55 4.4 30.2 1.0
HD12 A:LEU56 4.5 45.3 1.0
HG2 A:GLN53 4.5 27.2 1.0
HD11 A:LEU56 4.6 45.3 1.0
HG23 A:ILE223 4.6 58.8 1.0
CG A:TYR55 4.7 43.9 1.0
C10 A:M7I402 4.7 33.2 1.0
CD1 A:LEU56 4.7 43.3 1.0
HA A:ILE223 4.7 53.4 1.0
CD1 A:TYR224 4.8 47.8 1.0
NE2 A:GLN53 4.9 30.5 1.0
H6 A:M7I402 4.9 39.2 1.0
CE2 A:TYR224 4.9 50.6 1.0
HD21 A:LEU56 4.9 60.4 1.0
CE1 A:HIS217 5.0 35.3 1.0
C5 A:M7I402 5.0 34.4 1.0

Fluorine binding site 3 out of 6 in 7u9s

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Fluorine binding site 3 out of 6 in the Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor


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 D-Amino Acid Oxidase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:42.7
occ:1.00
F3 A:M7I402 0.0 42.7 1.0
C11 A:M7I402 1.3 34.4 1.0
F2 A:M7I402 2.2 47.1 1.0
F1 A:M7I402 2.2 43.1 1.0
C8 A:M7I402 2.3 42.4 1.0
HG A:LEU56 2.4 56.7 1.0
HE1 A:HIS217 2.5 37.3 1.0
HE21 A:GLN53 2.7 32.5 1.0
H7 A:M7I402 3.0 44.1 1.0
C7 A:M7I402 3.0 42.1 1.0
HD21 A:LEU56 3.0 60.4 1.0
HD11 A:LEU56 3.1 45.3 1.0
CE1 A:HIS217 3.2 35.3 1.0
CG A:LEU56 3.3 54.7 1.0
C9 A:M7I402 3.3 30.8 1.0
NE2 A:GLN53 3.4 30.5 1.0
H9 A:M7I402 3.5 32.8 1.0
CD1 A:LEU56 3.6 43.3 1.0
CD2 A:LEU56 3.6 58.4 1.0
HE22 A:GLN53 3.6 32.5 1.0
ND1 A:HIS217 3.8 38.1 1.0
HD12 A:LEU56 3.8 45.3 1.0
HA A:TYR55 3.9 44.7 1.0
HG22 A:ILE223 3.9 58.8 1.0
HD23 A:LEU56 4.0 60.4 1.0
NE2 A:HIS217 4.0 34.0 1.0
H1 A:HOH563 4.0 27.0 1.0
H A:LEU56 4.1 60.8 1.0
HE2 A:HIS217 4.1 36.0 1.0
O A:PRO54 4.2 27.4 1.0
HG2 A:GLN53 4.2 27.2 1.0
C6 A:M7I402 4.3 37.2 1.0
N A:LEU56 4.3 58.8 1.0
HG21 A:ILE223 4.5 58.8 1.0
C10 A:M7I402 4.5 33.2 1.0
HD13 A:LEU215 4.5 36.4 1.0
CB A:LEU56 4.5 53.4 1.0
HD22 A:LEU56 4.5 60.4 1.0
CD A:GLN53 4.6 28.6 1.0
HZ2 A:TRP107 4.6 44.1 1.0
HD13 A:LEU56 4.6 45.3 1.0
OD1 A:ASN96 4.7 25.9 1.0
CG2 A:ILE223 4.7 56.8 1.0
C A:TYR55 4.7 42.9 1.0
CA A:TYR55 4.8 42.7 1.0
CA A:LEU56 4.9 63.2 1.0
CG A:HIS217 4.9 38.1 1.0
HB A:ILE223 4.9 59.3 1.0
HA A:LEU56 4.9 65.2 1.0
HB2 A:LEU56 4.9 55.4 1.0
CG A:GLN53 4.9 25.2 1.0
O A:HOH563 4.9 25.0 1.0
C5 A:M7I402 4.9 34.4 1.0
CD2 A:HIS217 5.0 32.4 1.0
HE1 A:TYR224 5.0 45.7 1.0

Fluorine binding site 4 out of 6 in 7u9s

Go back to Fluorine Binding Sites List in 7u9s
Fluorine binding site 4 out of 6 in the Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor


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 Human D-Amino Acid Oxidase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:54.7
occ:1.00
F1 B:M7I402 0.0 54.7 1.0
C11 B:M7I402 1.3 45.3 1.0
F2 B:M7I402 2.2 50.3 1.0
F3 B:M7I402 2.2 52.3 1.0
C8 B:M7I402 2.4 47.0 1.0
H7 B:M7I402 2.4 44.3 1.0
HE1 B:HIS217 2.7 47.6 1.0
HB B:ILE223 2.7 61.4 1.0
C7 B:M7I402 2.7 42.3 1.0
HD11 B:LEU56 3.0 80.9 1.0
H2 B:HOH536 3.0 33.4 1.0
HD12 B:ILE223 3.1 61.9 1.0
HG B:LEU56 3.1 73.9 1.0
O B:HOH536 3.4 31.4 1.0
CE1 B:HIS217 3.4 45.6 1.0
HD13 B:ILE223 3.4 61.9 1.0
ND1 B:HIS217 3.5 52.0 1.0
CD1 B:ILE223 3.7 59.9 1.0
C9 B:M7I402 3.7 44.3 1.0
HG21 B:ILE223 3.7 70.5 1.0
CD1 B:LEU56 3.7 78.9 1.0
CB B:ILE223 3.7 59.4 1.0
HD12 B:LEU56 3.9 80.9 1.0
H B:TYR224 3.9 50.2 1.0
CG B:LEU56 3.9 71.9 1.0
H1 B:HOH536 3.9 33.4 1.0
HD21 B:LEU56 3.9 73.0 1.0
H9 B:M7I402 4.0 46.3 1.0
CG2 B:ILE223 4.1 68.5 1.0
HG22 B:ILE223 4.1 70.5 1.0
H B:LEU56 4.1 67.5 1.0
C6 B:M7I402 4.2 36.5 1.0
HA B:TYR55 4.3 59.4 1.0
CG1 B:ILE223 4.3 65.8 1.0
HE1 B:TYR224 4.4 51.2 1.0
CE1 B:TYR224 4.4 49.2 1.0
CD2 B:LEU56 4.4 71.0 1.0
HE21 B:GLN53 4.4 45.1 1.0
HA B:ILE223 4.4 61.4 1.0
NE2 B:HIS217 4.5 41.6 1.0
CD1 B:TYR224 4.6 39.0 1.0
HD11 B:ILE223 4.6 61.9 1.0
N B:TYR224 4.6 48.2 1.0
HD1 B:TYR224 4.6 41.0 1.0
HD13 B:LEU56 4.7 80.9 1.0
CA B:ILE223 4.7 59.4 1.0
H6 B:M7I402 4.8 38.5 1.0
HD23 B:LEU56 4.8 73.0 1.0
C10 B:M7I402 4.8 42.0 1.0
CG B:HIS217 4.9 43.9 1.0
H2 B:HOH530 4.9 52.0 1.0
CZ B:TYR224 4.9 54.7 1.0
HG13 B:ILE223 4.9 67.8 1.0
HD1 B:TYR55 5.0 72.8 1.0
N B:LEU56 5.0 65.5 1.0
HE2 B:HIS217 5.0 43.6 1.0
H2 B:HOH527 5.0 54.8 1.0

Fluorine binding site 5 out of 6 in 7u9s

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Fluorine binding site 5 out of 6 in the Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor


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 Human D-Amino Acid Oxidase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:50.3
occ:1.00
F2 B:M7I402 0.0 50.3 1.0
C11 B:M7I402 1.3 45.3 1.0
F1 B:M7I402 2.2 54.7 1.0
F3 B:M7I402 2.2 52.3 1.0
C8 B:M7I402 2.3 47.0 1.0
HA B:TYR55 2.5 59.4 1.0
H9 B:M7I402 2.7 46.3 1.0
HD12 B:ILE223 2.8 61.9 1.0
C9 B:M7I402 2.9 44.3 1.0
HD1 B:TYR55 3.0 72.8 1.0
HD13 B:ILE223 3.1 61.9 1.0
HG B:LEU56 3.4 73.9 1.0
H B:LEU56 3.4 67.5 1.0
CD1 B:ILE223 3.5 59.9 1.0
C7 B:M7I402 3.5 42.3 1.0
CA B:TYR55 3.6 57.4 1.0
HE1 B:TYR224 3.7 51.2 1.0
O B:PRO54 3.7 50.3 1.0
HH B:TYR224 3.8 82.4 1.0
H7 B:M7I402 3.8 44.3 1.0
OH B:TYR224 3.8 80.4 1.0
CD1 B:TYR55 3.9 70.8 1.0
CE1 B:TYR224 3.9 49.2 1.0
CZ B:TYR224 3.9 54.7 1.0
HD11 B:ILE223 3.9 61.9 1.0
HB B:ILE223 4.0 61.4 1.0
HE21 B:GLN53 4.0 45.1 1.0
N B:LEU56 4.2 65.5 1.0
HE1 B:HIS217 4.2 47.6 1.0
C10 B:M7I402 4.2 42.0 1.0
N B:TYR55 4.2 56.7 1.0
C B:PRO54 4.3 46.4 1.0
HG2 B:GLN53 4.3 45.7 1.0
C B:TYR55 4.3 58.2 1.0
CB B:TYR55 4.4 62.7 1.0
HB3 B:TYR55 4.4 64.7 1.0
CG B:LEU56 4.5 71.9 1.0
CG B:TYR55 4.5 68.0 1.0
HD11 B:LEU56 4.5 80.9 1.0
HG21 B:ILE223 4.6 70.5 1.0
CD1 B:TYR224 4.7 39.0 1.0
C6 B:M7I402 4.7 36.5 1.0
HE1 B:TYR55 4.7 69.1 1.0
CE1 B:TYR55 4.7 67.1 1.0
CE2 B:TYR224 4.7 56.6 1.0
CG1 B:ILE223 4.7 65.8 1.0
HD21 B:LEU56 4.8 73.0 1.0
CB B:ILE223 4.8 59.4 1.0
CD1 B:LEU56 4.9 78.9 1.0
H10 B:M7I402 4.9 44.0 1.0
HD12 B:LEU56 5.0 80.9 1.0
NE2 B:GLN53 5.0 43.1 1.0
HD23 B:LEU56 5.0 73.0 1.0
C5 B:M7I402 5.0 35.1 1.0
O B:GLN53 5.0 29.9 1.0

Fluorine binding site 6 out of 6 in 7u9s

Go back to Fluorine Binding Sites List in 7u9s
Fluorine binding site 6 out of 6 in the Crystal Structure of Human D-Amino Acid Oxidase in Complex with Inhibitor


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 Human D-Amino Acid Oxidase in Complex with Inhibitor within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:52.3
occ:1.00
F3 B:M7I402 0.0 52.3 1.0
C11 B:M7I402 1.3 45.3 1.0
F2 B:M7I402 2.2 50.3 1.0
F1 B:M7I402 2.2 54.7 1.0
C8 B:M7I402 2.3 47.0 1.0
HE21 B:GLN53 2.4 45.1 1.0
HG B:LEU56 2.5 73.9 1.0
HE1 B:HIS217 2.7 47.6 1.0
HD21 B:LEU56 2.9 73.0 1.0
H9 B:M7I402 2.9 46.3 1.0
C9 B:M7I402 3.0 44.3 1.0
HD23 B:LEU56 3.2 73.0 1.0
NE2 B:GLN53 3.3 43.1 1.0
CD2 B:LEU56 3.3 71.0 1.0
CG B:LEU56 3.3 71.9 1.0
C7 B:M7I402 3.4 42.3 1.0
CE1 B:HIS217 3.5 45.6 1.0
HD11 B:LEU56 3.5 80.9 1.0
H7 B:M7I402 3.6 44.3 1.0
H B:LEU56 3.6 67.5 1.0
HA B:TYR55 3.6 59.4 1.0
HG2 B:GLN53 3.6 45.7 1.0
HE22 B:GLN53 3.6 45.1 1.0
O B:PRO54 3.9 50.3 1.0
CD1 B:LEU56 4.0 78.9 1.0
N B:LEU56 4.1 65.5 1.0
HZ2 B:TRP107 4.1 48.3 1.0
NE2 B:HIS217 4.2 41.6 1.0
HE2 B:HIS217 4.2 43.6 1.0
ND1 B:HIS217 4.2 52.0 1.0
C10 B:M7I402 4.3 42.0 1.0
CD B:GLN53 4.3 40.3 1.0
HD22 B:LEU56 4.4 73.0 1.0
HD13 B:LEU215 4.4 39.3 1.0
CG B:GLN53 4.4 43.7 1.0
HD12 B:LEU56 4.5 80.9 1.0
CA B:TYR55 4.5 57.4 1.0
C6 B:M7I402 4.6 36.5 1.0
C B:TYR55 4.6 58.2 1.0
CB B:LEU56 4.6 68.8 1.0
H2 B:HOH536 4.6 33.4 1.0
HD12 B:ILE223 4.6 61.9 1.0
HD13 B:ILE223 4.6 61.9 1.0
OD1 B:ASN96 4.6 35.1 1.0
HA B:LEU56 4.7 74.8 1.0
CA B:LEU56 4.7 72.8 1.0
HB B:ILE223 4.8 61.4 1.0
HD13 B:LEU56 4.8 80.9 1.0
C B:PRO54 4.9 46.4 1.0
HE1 B:TYR224 4.9 51.2 1.0
C5 B:M7I402 4.9 35.1 1.0
HD1 B:TYR55 4.9 72.8 1.0
HZ3 B:TRP132 4.9 59.6 1.0

Reference:

H.Tang, K.Jensen, E.Houang, F.M.Mcrobb, S.Bhat, M.Svensson, A.Bochevarov, T.Day, M.K.Dahlgren, J.A.Bell, L.Frye, R.J.Skene, J.H.Lewis, J.D.Osborne, J.P.Tierney, J.A.Gordon, M.A.Palomero, C.Gallati, R.S.L.Chapman, D.R.Jones, K.L.Hirst, M.Sephton, A.Chauhan, A.Sharpe, P.Tardia, E.A.Dechaux, A.Taylor, R.D.Waddell, A.Valentine, H.B.Janssens, O.Aziz, D.E.Bloomfield, S.Ladha, I.J.Fraser, J.M.Ellard. Discovery of A Novel Class of D-Amino Acid Oxidase Inhibitors Using the Schrodinger Computational Platform. J.Med.Chem. V. 65 6775 2022.
ISSN: ISSN 0022-2623
PubMed: 35482677
DOI: 10.1021/ACS.JMEDCHEM.2C00118
Page generated: Wed Jul 16 00:53:16 2025

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