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Fluorine in PDB 6pyy: Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site

Enzymatic activity of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site

All present enzymatic activity of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site:
1.13.11.11;

Protein crystallography data

The structure of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site, PDB code: 6pyy was solved by K.N.Pham, A.Lewis-Ballester, S.R.Yeh, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 29.90 / 2.40
Space group P 21 21 2
Cell size a, b, c (Å), α, β, γ (°) 144.188, 154.037, 87.973, 90.00, 90.00, 90.00
R / Rfree (%) 19.1 / 23.8

Other elements in 6pyy:

The structure of Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site also contains other interesting chemical elements:

Iron (Fe) 4 atoms

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site (pdb code 6pyy). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 8 binding sites of Fluorine where determined in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site, PDB code: 6pyy:
Jump to Fluorine binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Fluorine binding site 1 out of 8 in 6pyy

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Fluorine binding site 1 out of 8 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site


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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F402

b:84.7
occ:1.00
 F8 A:H7S402 0.0 84.7 1.0
CZ3 A:H7S402 1.3 67.4 1.0
CH2 A:H7S402 2.3 60.2 1.0
CE3 A:H7S402 2.4 63.5 1.0
CD2 B:TYR45 3.0 51.2 1.0
CB A:ALA150 3.3 70.8 1.0
CD2 A:H7S402 3.6 66.4 1.0
CE2 B:TYR45 3.6 49.9 1.0
CZ2 A:H7S402 3.6 63.5 1.0
CG B:TYR45 3.8 48.0 1.0
CD2 A:LEU147 3.9 64.2 1.0
CB B:TYR45 4.0 41.0 1.0
C A:ALA150 4.1 65.8 1.0
CE2 A:H7S402 4.1 66.1 1.0
O A:ALA150 4.3 65.6 1.0
CA A:ALA150 4.3 71.8 1.0
CA B:TYR42 4.3 44.7 1.0
N A:SER151 4.4 63.0 1.0
O A:LEU147 4.5 61.1 1.0
CB A:LEU147 4.6 64.6 1.0
CZ B:TYR45 4.7 49.2 1.0
CD1 B:TYR42 4.7 41.3 1.0
CD2 B:LEU40 4.7 58.5 1.0
CG A:LEU147 4.8 60.5 1.0
CD1 B:TYR45 4.8 50.0 1.0
CE2 A:PHE72 4.8 39.7 1.0
N B:TYR42 4.9 46.9 1.0
CA A:SER151 4.9 67.9 1.0
CA A:LEU147 4.9 64.5 1.0
CG A:H7S402 5.0 75.2 1.0
CB B:TYR42 5.0 43.1 1.0

Fluorine binding site 2 out of 8 in 6pyy

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Fluorine binding site 2 out of 8 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site


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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F403

b:67.2
occ:1.00
 F8 A:H7S403 0.0 67.2 1.0
CZ3 A:H7S403 1.3 53.0 1.0
CH2 A:H7S403 2.3 49.8 1.0
CE3 A:H7S403 2.3 48.8 1.0
O A:ARG303 2.9 39.9 1.0
O A:HOH518 3.5 41.9 1.0
CE1 A:PHE304 3.5 45.0 1.0
CD1 A:PHE304 3.5 44.2 1.0
CD2 A:H7S403 3.5 50.5 1.0
CZ2 A:H7S403 3.5 50.6 1.0
C A:ARG303 3.8 42.2 1.0
O A:HOH610 3.8 52.3 1.0
CG A:PRO307 3.9 38.2 1.0
CE2 A:H7S403 4.0 50.3 1.0
CB A:ARG303 4.0 61.4 1.0
OE2 A:GLU105 4.2 60.9 1.0
CD A:PRO213 4.3 45.5 1.0
NE A:ARG303 4.4 66.8 1.0
CG A:PRO213 4.4 45.7 1.0
NH2 A:ARG303 4.5 61.1 1.0
CA A:ARG303 4.5 50.5 1.0
N A:PHE304 4.6 39.0 1.0
CZ A:ARG303 4.6 63.9 1.0
CD A:GLU105 4.6 59.0 1.0
CZ A:PHE304 4.7 43.7 1.0
CG A:PHE304 4.7 42.1 1.0
CA A:PHE304 4.7 39.8 1.0
CB A:PRO307 4.8 38.4 1.0
CG A:ARG303 4.9 65.9 1.0
OE1 A:GLU105 5.0 64.8 1.0
CG A:H7S403 5.0 57.4 1.0

Fluorine binding site 3 out of 8 in 6pyy

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Fluorine binding site 3 out of 8 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site


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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F402

b:75.5
occ:1.00
 F8 B:H7S402 0.0 75.5 1.0
CZ3 B:H7S402 1.3 55.5 1.0
CH2 B:H7S402 2.3 55.6 1.0
CE3 B:H7S402 2.4 52.4 1.0
CD2 A:TYR45 3.3 44.0 1.0
CB B:ALA150 3.3 58.0 1.0
CD2 B:H7S402 3.6 51.4 1.0
CZ2 B:H7S402 3.6 54.3 1.0
CG A:TYR45 3.6 45.4 1.0
CB A:TYR45 3.8 44.9 1.0
CE2 A:TYR45 4.0 42.8 1.0
CE2 B:H7S402 4.1 56.5 1.0
CA A:TYR42 4.3 43.9 1.0
CG B:LEU147 4.3 52.1 1.0
C B:ALA150 4.3 54.7 1.0
CA B:ALA150 4.5 57.7 1.0
N B:SER151 4.5 52.3 1.0
CD1 A:TYR45 4.5 42.0 1.0
O B:LEU147 4.6 52.9 1.0
O B:ALA150 4.6 50.6 1.0
N A:TYR42 4.7 47.2 1.0
CB B:LEU147 4.7 51.2 1.0
CD1 A:TYR42 4.7 39.8 1.0
CD2 A:LEU40 4.8 67.3 1.0
CZ A:TYR45 4.8 46.0 1.0
CD1 B:LEU147 4.9 53.9 1.0
CB A:TYR42 4.9 41.4 1.0
CA B:LEU147 4.9 50.5 1.0
CG B:H7S402 5.0 58.6 1.0
O A:TYR42 5.0 47.8 1.0

Fluorine binding site 4 out of 8 in 6pyy

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Fluorine binding site 4 out of 8 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site


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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F403

b:86.1
occ:1.00
 F8 B:H7S403 0.0 86.1 1.0
CZ3 B:H7S403 1.3 60.7 1.0
CE3 B:H7S403 2.3 60.8 1.0
CH2 B:H7S403 2.4 51.8 1.0
O B:ARG303 2.8 38.6 1.0
O B:HOH517 3.1 43.2 1.0
O B:HOH601 3.3 47.6 1.0
CD2 B:H7S403 3.6 53.1 1.0
CZ2 B:H7S403 3.6 48.6 1.0
C B:ARG303 3.6 44.5 1.0
CD1 B:PHE304 3.8 47.0 1.0
OE1 B:GLU105 3.9 65.5 1.0
CE1 B:PHE304 3.9 48.0 1.0
CB B:ARG303 3.9 56.8 1.0
CG B:PRO307 4.0 39.6 1.0
CE2 B:H7S403 4.1 50.1 1.0
CA B:ARG303 4.3 49.5 1.0
CD B:GLU105 4.3 64.6 1.0
NE B:ARG303 4.4 69.8 1.0
CG B:PRO213 4.4 41.0 1.0
N B:PHE304 4.5 41.2 1.0
CD B:PRO213 4.5 40.8 1.0
NH2 B:ARG303 4.6 65.6 1.0
CZ B:ARG303 4.7 65.6 1.0
CG B:ARG303 4.7 73.1 1.0
OE2 B:GLU105 4.8 68.9 1.0
CA B:PHE304 4.8 41.6 1.0
CB B:PRO307 4.8 39.1 1.0
CG B:PHE304 4.9 42.8 1.0
CG B:H7S403 5.0 59.5 1.0
CG B:GLU105 5.0 56.8 1.0

Fluorine binding site 5 out of 8 in 6pyy

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Fluorine binding site 5 out of 8 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site


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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F402

b:69.0
occ:1.00
 F8 C:H7S402 0.0 69.0 1.0
CZ3 C:H7S402 1.3 62.4 1.0
CH2 C:H7S402 2.3 61.1 1.0
CE3 C:H7S402 2.3 62.6 1.0
CD2 D:TYR45 3.2 48.4 1.0
CB C:ALA150 3.2 54.6 1.0
CD2 C:H7S402 3.6 71.8 1.0
CZ2 C:H7S402 3.6 64.1 1.0
CG D:TYR45 3.7 49.0 1.0
CE2 D:TYR45 3.8 54.0 1.0
CB D:TYR45 4.0 45.6 1.0
CE2 C:H7S402 4.1 70.0 1.0
C C:ALA150 4.2 63.5 1.0
CA D:TYR42 4.2 49.4 1.0
CA C:ALA150 4.3 60.2 1.0
N C:SER151 4.4 61.5 1.0
CD2 C:LEU147 4.4 57.6 1.0
O C:ALA150 4.6 62.9 1.0
CB C:LEU147 4.6 55.7 1.0
O C:LEU147 4.7 54.9 1.0
CD2 D:TYR42 4.7 50.8 1.0
CD1 D:TYR45 4.7 50.3 1.0
CZ D:TYR45 4.7 50.9 1.0
N D:TYR42 4.8 49.5 1.0
CB D:TYR42 4.8 54.6 1.0
CE2 C:PHE72 4.9 36.9 1.0
CG C:LEU147 4.9 56.5 1.0
CG C:H7S402 4.9 79.1 1.0
CD2 D:LEU40 5.0 72.1 1.0
O D:TYR42 5.0 47.1 1.0
CA C:LEU147 5.0 57.0 1.0

Fluorine binding site 6 out of 8 in 6pyy

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Fluorine binding site 6 out of 8 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site


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 Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe atom residue distance (Å) B Occ
C:F403

b:86.5
occ:1.00
 F8 C:H7S403 0.0 86.5 1.0
CZ3 C:H7S403 1.3 64.7 1.0
CH2 C:H7S403 2.3 64.3 1.0
CE3 C:H7S403 2.4 62.0 1.0
O C:ARG303 2.8 40.7 1.0
CD1 C:PHE304 3.3 52.7 1.0
CE1 C:PHE304 3.4 53.0 1.0
CD2 C:H7S403 3.6 68.0 1.0
CZ2 C:H7S403 3.6 62.0 1.0
C C:ARG303 3.6 50.0 1.0
O C:HOH577 3.8 52.1 1.0
CG C:PRO307 3.9 45.4 1.0
CB C:ARG303 4.0 59.8 1.0
CE2 C:H7S403 4.1 65.9 1.0
CA C:ARG303 4.4 49.9 1.0
N C:PHE304 4.4 51.0 1.0
OE2 C:GLU105 4.5 62.7 1.0
CA C:PHE304 4.5 51.5 1.0
CG C:PHE304 4.5 50.7 1.0
NE C:ARG303 4.6 72.2 1.0
CB C:PRO307 4.6 45.6 1.0
CD C:PRO213 4.6 70.3 1.0
CZ C:PHE304 4.6 52.9 1.0
CG C:PRO213 4.7 74.2 1.0
NH2 C:ARG303 4.7 68.3 1.0
CD C:GLU105 4.9 68.5 1.0
CZ C:ARG303 4.9 70.2 1.0
CD C:PRO307 4.9 47.9 1.0
CG C:ARG303 5.0 76.5 1.0

Fluorine binding site 7 out of 8 in 6pyy

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Fluorine binding site 7 out of 8 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site


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 Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F402

b:72.8
occ:1.00
 F8 D:H7S402 0.0 72.8 1.0
CZ3 D:H7S402 1.3 63.1 1.0
CH2 D:H7S402 2.3 59.2 1.0
CE3 D:H7S402 2.3 58.7 1.0
CD2 C:TYR45 3.2 38.4 1.0
CB D:ALA150 3.4 44.0 1.0
CD2 D:H7S402 3.6 62.0 1.0
CZ2 D:H7S402 3.6 62.4 1.0
CG C:TYR45 3.7 41.6 1.0
CE2 C:TYR45 3.8 41.1 1.0
CB C:TYR45 4.0 42.7 1.0
CE2 D:H7S402 4.1 63.5 1.0
CD2 D:LEU147 4.2 52.1 1.0
CB D:LEU147 4.3 49.9 1.0
C D:ALA150 4.4 48.3 1.0
O D:LEU147 4.4 53.1 1.0
CA C:TYR42 4.4 44.1 1.0
CA D:ALA150 4.5 48.1 1.0
CD1 C:TYR45 4.5 40.6 1.0
CZ C:TYR45 4.6 37.6 1.0
O D:ALA150 4.6 48.4 1.0
CD2 C:LEU40 4.6 69.2 1.0
CD1 C:TYR42 4.7 43.5 1.0
N D:SER151 4.7 51.1 1.0
CG D:LEU147 4.7 47.7 1.0
CE2 D:PHE72 4.8 39.3 1.0
CA D:LEU147 4.9 51.4 1.0
N C:TYR42 4.9 45.9 1.0
CG D:H7S402 4.9 69.4 1.0
CE1 C:TYR45 4.9 37.2 1.0
CB C:TYR42 4.9 46.1 1.0

Fluorine binding site 8 out of 8 in 6pyy

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Fluorine binding site 8 out of 8 in the Crystal Structure of Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site


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 Human Tryptophan 2,3-Dioxygenase in Complex with Pf-06840003 in Active Site and Exo Site within 5.0Å range:
probe atom residue distance (Å) B Occ
D:F403

b:78.5
occ:1.00
 F8 D:H7S403 0.0 78.5 1.0
CZ3 D:H7S403 1.3 63.6 1.0
CE3 D:H7S403 2.3 64.6 1.0
CH2 D:H7S403 2.4 58.9 1.0
O D:ARG303 2.7 43.5 1.0
CD1 D:PHE304 3.6 47.7 1.0
C D:ARG303 3.6 46.1 1.0
CD2 D:H7S403 3.6 67.3 1.0
CZ2 D:H7S403 3.6 60.8 1.0
CE1 D:PHE304 3.7 47.8 1.0
O D:HOH588 3.7 50.8 1.0
CG D:PRO307 3.8 42.1 1.0
CD D:ARG303 3.9 80.8 1.0
CG D:ARG303 4.0 69.6 1.0
CB D:ARG303 4.0 59.5 1.0
CE2 D:H7S403 4.1 62.9 1.0
NH2 D:ARG303 4.1 91.4 1.0
CA D:ARG303 4.3 50.4 1.0
N D:PHE304 4.4 42.3 1.0
CG D:PRO213 4.5 57.8 1.0
CA D:PHE304 4.6 40.1 1.0
CG D:PHE304 4.7 42.6 1.0
CB D:PRO307 4.7 41.7 1.0
CD D:PRO213 4.8 58.9 1.0
CZ D:PHE304 4.9 42.9 1.0
CD D:PRO307 4.9 40.2 1.0
NE D:ARG303 4.9 80.2 1.0

Reference:

K.N.Pham, A.Lewis-Ballester, S.R.Yeh. Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase. J.Am.Chem.Soc. V. 141 18771 2019.
ISSN: ESSN 1520-5126
PubMed: 31682426
DOI: 10.1021/JACS.9B08871
Page generated: Fri Aug 2 00:31:34 2024

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