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Manganese in PDB 6zbo: Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat)

Enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat)

All present enzymatic activity of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat):
1.14.11.29;

Protein crystallography data

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat), PDB code: 6zbo was solved by W.D.Figg Jr, M.A.Mcdonough, Y.Nakashima, J.P.Holt-Martyn, C.J.Schofield, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 53.71 / 1.79
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 77.119, 75.151, 127.215, 90, 95.31, 90
R / Rfree (%) 18 / 20.6

Other elements in 6zbo:

The structure of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat) also contains other interesting chemical elements:

Chlorine (Cl) 13 atoms

Manganese Binding Sites:

The binding sites of Manganese atom in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat) (pdb code 6zbo). This binding sites where shown within 5.0 Angstroms radius around Manganese atom.
In total 6 binding sites of Manganese where determined in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat), PDB code: 6zbo:
Jump to Manganese binding site number: 1; 2; 3; 4; 5; 6;

Manganese binding site 1 out of 6 in 6zbo

Go back to Manganese Binding Sites List in 6zbo
Manganese binding site 1 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 1 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mn601

b:28.7
occ:1.00
 N05 A:QEQ602 2.2 32.1 1.0
NE2 A:HIS374 2.2 29.2 1.0
NE2 A:HIS313 2.2 31.4 1.0
O A:HOH748 2.2 29.2 1.0
N16 A:QEQ602 2.3 32.1 1.0
OD1 A:ASP315 2.3 32.1 1.0
N03 A:QEQ602 3.0 33.4 1.0
CE1 A:HIS374 3.0 29.8 1.0
C04 A:QEQ602 3.0 34.8 1.0
HE1 A:HIS374 3.1 35.9 1.0
C06 A:QEQ602 3.1 34.5 1.0
CE1 A:HIS313 3.1 33.8 1.0
H061 A:QEQ602 3.2 41.5 1.0
HE1 A:HIS313 3.3 40.6 1.0
CD2 A:HIS313 3.3 31.5 1.0
CG A:ASP315 3.3 31.3 1.0
CD2 A:HIS374 3.3 28.8 1.0
C17 A:QEQ602 3.4 33.1 1.0
HD2 A:HIS313 3.5 37.9 1.0
HD2 A:HIS374 3.5 34.6 1.0
OD2 A:ASP315 3.6 32.2 1.0
H171 A:QEQ602 3.7 39.8 1.0
HZ A:PHE366 4.1 34.4 1.0
O A:HOH793 4.1 32.7 1.0
ND1 A:HIS374 4.2 29.6 1.0
ND1 A:HIS313 4.3 32.1 1.0
C02 A:QEQ602 4.3 35.0 1.0
C15 A:QEQ602 4.3 35.7 1.0
HZ2 A:TRP389 4.3 37.2 1.0
CG A:HIS374 4.3 29.3 1.0
CG A:HIS313 4.4 32.9 1.0
HA A:ASP315 4.4 37.4 1.0
C18 A:QEQ602 4.5 34.4 1.0
N07 A:QEQ602 4.5 35.6 1.0
CB A:ASP315 4.6 30.8 1.0
HG21 A:THR325 4.9 36.4 1.0
CA A:ASP315 4.9 31.1 1.0
C08 A:QEQ602 4.9 36.8 1.0
CZ A:PHE366 4.9 28.6 1.0
HD1 A:HIS374 4.9 35.6 1.0
H A:ASP315 5.0 37.3 1.0
H151 A:QEQ602 5.0 42.9 1.0
HE1 A:PHE366 5.0 35.7 1.0

Manganese binding site 2 out of 6 in 6zbo

Go back to Manganese Binding Sites List in 6zbo
Manganese binding site 2 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 2 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mn601

b:30.9
occ:1.00
 O B:HOH725 2.1 27.9 1.0
N16 B:QEQ602 2.2 33.5 1.0
NE2 B:HIS374 2.2 29.7 1.0
NE2 B:HIS313 2.3 33.7 1.0
N05 B:QEQ602 2.3 28.5 1.0
OD1 B:ASP315 2.3 34.1 1.0
N03 B:QEQ602 3.0 32.7 1.0
CE1 B:HIS374 3.1 32.6 1.0
C04 B:QEQ602 3.1 34.5 1.0
CG B:ASP315 3.1 32.6 1.0
C06 B:QEQ602 3.2 33.2 1.0
CE1 B:HIS313 3.2 34.0 1.0
HE1 B:HIS374 3.2 39.3 1.0
H061 B:QEQ602 3.2 39.9 1.0
OD2 B:ASP315 3.2 31.0 1.0
CD2 B:HIS313 3.3 33.9 1.0
HE1 B:HIS313 3.3 40.9 1.0
CD2 B:HIS374 3.3 32.8 1.0
C17 B:QEQ602 3.4 33.4 1.0
HD2 B:HIS313 3.5 40.8 1.0
HD2 B:HIS374 3.5 39.4 1.0
H171 B:QEQ602 3.8 40.1 1.0
HZ B:PHE366 4.0 40.1 1.0
O B:HOH765 4.1 31.1 1.0
HZ2 B:TRP389 4.2 41.0 1.0
ND1 B:HIS374 4.3 33.3 1.0
ND1 B:HIS313 4.3 34.9 1.0
C02 B:QEQ602 4.3 35.6 1.0
C15 B:QEQ602 4.4 34.9 1.0
CG B:HIS313 4.4 35.6 1.0
CG B:HIS374 4.4 32.7 1.0
HA B:ASP315 4.5 39.9 1.0
C18 B:QEQ602 4.5 34.1 1.0
CB B:ASP315 4.5 33.3 1.0
N07 B:QEQ602 4.5 35.6 1.0
HG21 B:THR325 4.8 38.3 1.0
CA B:ASP315 4.9 33.2 1.0
HB3 B:ASP315 4.9 40.1 1.0
CZ B:PHE366 4.9 33.3 1.0
C08 B:QEQ602 4.9 35.5 1.0

Manganese binding site 3 out of 6 in 6zbo

Go back to Manganese Binding Sites List in 6zbo
Manganese binding site 3 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 3 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat) within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mn601

b:33.4
occ:1.00
 N16 C:QEQ602 2.2 34.9 1.0
N05 C:QEQ602 2.2 36.9 1.0
OD1 C:ASP315 2.2 34.7 1.0
NE2 C:HIS313 2.2 34.4 1.0
NE2 C:HIS374 2.3 35.2 1.0
O C:HOH730 2.3 32.3 1.0
N03 C:QEQ602 3.0 36.4 1.0
C04 C:QEQ602 3.0 38.8 1.0
CE1 C:HIS374 3.2 35.0 1.0
C06 C:QEQ602 3.2 37.5 1.0
CE1 C:HIS313 3.2 37.0 1.0
CG C:ASP315 3.2 34.1 1.0
CD2 C:HIS313 3.2 36.3 1.0
H061 C:QEQ602 3.3 45.1 1.0
HE1 C:HIS374 3.3 42.2 1.0
CD2 C:HIS374 3.3 34.6 1.0
HE1 C:HIS313 3.3 44.5 1.0
C17 C:QEQ602 3.4 38.0 1.0
HD2 C:HIS313 3.4 43.7 1.0
OD2 C:ASP315 3.5 33.6 1.0
HD2 C:HIS374 3.5 41.6 1.0
H171 C:QEQ602 3.7 45.7 1.0
HZ C:PHE366 4.1 40.6 1.0
O C:HOH743 4.2 34.4 1.0
HZ2 C:TRP389 4.2 44.2 1.0
C02 C:QEQ602 4.2 37.2 1.0
ND1 C:HIS313 4.3 35.4 1.0
ND1 C:HIS374 4.3 36.3 1.0
C15 C:QEQ602 4.3 39.6 1.0
CG C:HIS313 4.4 36.4 1.0
HA C:ASP315 4.4 42.0 1.0
CG C:HIS374 4.4 34.5 1.0
C18 C:QEQ602 4.4 39.6 1.0
N07 C:QEQ602 4.5 38.7 1.0
CB C:ASP315 4.6 34.3 1.0
HG21 C:THR325 4.9 41.2 1.0
CA C:ASP315 4.9 34.9 1.0
C08 C:QEQ602 5.0 39.7 1.0
H C:ASP315 5.0 41.5 1.0
H151 C:QEQ602 5.0 47.7 1.0

Manganese binding site 4 out of 6 in 6zbo

Go back to Manganese Binding Sites List in 6zbo
Manganese binding site 4 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 4 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat) within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mn601

b:34.0
occ:1.00
 NE2 D:HIS313 2.1 34.6 1.0
O D:HOH719 2.2 35.1 1.0
NE2 D:HIS374 2.2 33.4 1.0
N05 D:QEQ602 2.3 33.7 1.0
N16 D:QEQ602 2.3 39.2 1.0
OD1 D:ASP315 2.3 38.3 1.0
N03 D:QEQ602 3.0 39.0 1.0
CE1 D:HIS313 3.1 37.5 1.0
CE1 D:HIS374 3.1 38.5 1.0
C04 D:QEQ602 3.1 39.5 1.0
CD2 D:HIS313 3.1 36.2 1.0
CG D:ASP315 3.1 37.9 1.0
C06 D:QEQ602 3.2 37.7 1.0
HE1 D:HIS374 3.2 46.3 1.0
H061 D:QEQ602 3.2 45.4 1.0
HE1 D:HIS313 3.2 45.1 1.0
CD2 D:HIS374 3.3 36.9 1.0
OD2 D:ASP315 3.3 42.6 1.0
HD2 D:HIS313 3.3 43.6 1.0
C17 D:QEQ602 3.5 40.0 1.0
HD2 D:HIS374 3.5 44.3 1.0
H171 D:QEQ602 3.8 48.1 1.0
HZ D:PHE366 4.1 45.1 1.0
O D:HOH751 4.1 39.1 1.0
ND1 D:HIS313 4.2 36.0 1.0
CG D:HIS313 4.2 35.8 1.0
ND1 D:HIS374 4.2 34.0 1.0
HZ2 D:TRP389 4.3 47.3 1.0
C02 D:QEQ602 4.3 43.0 1.0
C15 D:QEQ602 4.4 39.1 1.0
CG D:HIS374 4.4 36.2 1.0
HA D:ASP315 4.5 44.4 1.0
C18 D:QEQ602 4.5 43.1 1.0
CB D:ASP315 4.5 37.7 1.0
N07 D:QEQ602 4.5 39.8 1.0
HG21 D:THR325 4.8 47.2 1.0
HB3 D:ASP315 4.9 45.3 1.0
CA D:ASP315 4.9 36.9 1.0
HD1 D:HIS313 4.9 43.3 1.0
C08 D:QEQ602 5.0 40.3 1.0
H D:ASP315 5.0 42.5 1.0
HD1 D:HIS374 5.0 40.9 1.0
CZ D:PHE366 5.0 37.5 1.0

Manganese binding site 5 out of 6 in 6zbo

Go back to Manganese Binding Sites List in 6zbo
Manganese binding site 5 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 5 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat) within 5.0Å range:
probe atom residue distance (Å) B Occ
E:Mn601

b:39.0
occ:1.00
 N05 E:QEQ602 2.1 41.9 1.0
OD1 E:ASP315 2.1 40.2 1.0
NE2 E:HIS374 2.2 41.3 1.0
N16 E:QEQ602 2.2 42.5 1.0
NE2 E:HIS313 2.2 39.8 1.0
O E:HOH714 2.3 39.0 1.0
N03 E:QEQ602 2.9 42.4 1.0
C04 E:QEQ602 2.9 43.4 1.0
CE1 E:HIS374 3.0 42.5 1.0
HE1 E:HIS374 3.0 51.1 1.0
C06 E:QEQ602 3.1 43.0 1.0
CG E:ASP315 3.1 41.3 1.0
H061 E:QEQ602 3.2 51.7 1.0
CE1 E:HIS313 3.2 42.8 1.0
CD2 E:HIS313 3.2 41.1 1.0
CD2 E:HIS374 3.3 43.2 1.0
HD2 E:HIS313 3.4 49.4 1.0
HE1 E:HIS313 3.4 51.4 1.0
C17 E:QEQ602 3.4 43.0 1.0
OD2 E:ASP315 3.4 42.0 1.0
HD2 E:HIS374 3.5 52.0 1.0
H171 E:QEQ602 3.7 51.7 1.0
O E:HOH747 4.1 44.2 1.0
HZ E:PHE366 4.1 48.5 1.0
ND1 E:HIS374 4.2 41.5 1.0
C02 E:QEQ602 4.2 44.5 1.0
C15 E:QEQ602 4.2 46.1 1.0
HZ2 E:TRP389 4.3 54.7 1.0
ND1 E:HIS313 4.3 40.6 1.0
CG E:HIS374 4.3 42.5 1.0
CG E:HIS313 4.3 40.9 1.0
HA E:ASP315 4.4 49.0 1.0
C18 E:QEQ602 4.4 44.7 1.0
N07 E:QEQ602 4.4 45.0 1.0
CB E:ASP315 4.5 41.2 1.0
C08 E:QEQ602 4.8 46.0 1.0
CA E:ASP315 4.9 40.7 1.0
H151 E:QEQ602 4.9 55.4 1.0
HG21 E:THR325 4.9 56.4 1.0
HD1 E:HIS374 4.9 50.0 1.0
CZ E:PHE366 5.0 40.3 1.0
H E:ASP315 5.0 48.7 1.0
HE1 E:PHE366 5.0 49.9 1.0

Manganese binding site 6 out of 6 in 6zbo

Go back to Manganese Binding Sites List in 6zbo
Manganese binding site 6 out of 6 in the Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat)


Mono view


Stereo pair view

A full contact list of Manganese with other atoms in the Mn binding site number 6 of Hif Prolyl Hydroxylase 2 (PHD2/EGLN1) in Complex with 1-(6- Morpholinopyrimidin-4-Yl)-4-(1H-1,2,3-Triazol-1-Yl)-1H-Pyrazol-5-Ol (Molidustat) within 5.0Å range:
probe atom residue distance (Å) B Occ
F:Mn601

b:35.0
occ:1.00
 N16 F:QEQ602 2.2 38.3 1.0
O F:HOH708 2.2 36.6 1.0
OD1 F:ASP315 2.2 36.7 1.0
NE2 F:HIS374 2.2 33.9 1.0
NE2 F:HIS313 2.3 34.4 1.0
N05 F:QEQ602 2.3 39.1 1.0
N03 F:QEQ602 3.0 38.7 1.0
CE1 F:HIS374 3.1 34.8 1.0
C04 F:QEQ602 3.1 39.7 1.0
HE1 F:HIS374 3.2 41.9 1.0
CG F:ASP315 3.2 36.8 1.0
CE1 F:HIS313 3.2 34.7 1.0
C06 F:QEQ602 3.3 40.4 1.0
CD2 F:HIS313 3.3 35.6 1.0
CD2 F:HIS374 3.3 33.7 1.0
C17 F:QEQ602 3.3 38.8 1.0
H061 F:QEQ602 3.3 48.6 1.0
HE1 F:HIS313 3.4 41.7 1.0
HD2 F:HIS313 3.4 42.8 1.0
OD2 F:ASP315 3.5 37.1 1.0
HD2 F:HIS374 3.5 40.5 1.0
H171 F:QEQ602 3.6 46.6 1.0
O F:HOH756 4.1 41.0 1.0
HZ F:PHE366 4.1 44.3 1.0
ND1 F:HIS374 4.2 33.4 1.0
C02 F:QEQ602 4.2 40.4 1.0
HZ2 F:TRP389 4.3 49.3 1.0
C15 F:QEQ602 4.3 42.8 1.0
ND1 F:HIS313 4.3 34.0 1.0
CG F:HIS374 4.4 33.4 1.0
HA F:ASP315 4.4 43.8 1.0
C18 F:QEQ602 4.4 39.3 1.0
CG F:HIS313 4.4 34.3 1.0
CB F:ASP315 4.6 36.7 1.0
N07 F:QEQ602 4.6 45.9 1.0
HG21 F:THR325 4.8 48.5 1.0
CA F:ASP315 4.9 36.4 1.0
H F:ASP315 5.0 41.5 1.0
CZ F:PHE366 5.0 36.8 1.0
HD1 F:HIS374 5.0 40.2 1.0
C08 F:QEQ602 5.0 45.0 1.0

Reference:

W.D.Figg Jr, Y.Nakashima, M.A.Mcdonough, J.P.Holt-Martyn, A.Krajnc, C.J.Schofield. Co-Crystal Structure of PHD2 with Molidustat and IOX4 Chemmedchem 2021.
ISSN: ESSN 1860-7187
DOI: 10.1002/CMDC.202100133
Page generated: Sun Oct 6 07:58:11 2024

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