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Iron in PDB 6pu7: Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide)

Enzymatic activity of Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide)

All present enzymatic activity of Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide):
1.13.11.52;

Protein crystallography data

The structure of Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide), PDB code: 6pu7 was solved by C.A.Lesburg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.00 / 2.43
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 86.427, 96.516, 127.725, 90.00, 90.00, 90.00
R / Rfree (%) 20 / 25

Other elements in 6pu7:

The structure of Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide) also contains other interesting chemical elements:

Fluorine (F) 2 atoms

Iron Binding Sites:

The binding sites of Iron atom in the Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide) (pdb code 6pu7). This binding sites where shown within 5.0 Angstroms radius around Iron atom.
In total 2 binding sites of Iron where determined in the Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide), PDB code: 6pu7:
Jump to Iron binding site number: 1; 2;

Iron binding site 1 out of 2 in 6pu7

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Iron binding site 1 out of 2 in the Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 1 of Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Fe501

b:32.9
occ:1.00
 FE A:HEM501 0.0 32.9 1.0
NA A:HEM501 2.0 33.3 1.0
ND A:HEM501 2.1 35.1 1.0
NC A:HEM501 2.1 35.4 1.0
NB A:HEM501 2.1 35.0 1.0
NE2 A:HIS346 2.2 27.0 1.0
O11 A:OY4502 2.4 54.2 1.0
C1A A:HEM501 3.0 34.7 1.0
C4A A:HEM501 3.0 33.6 1.0
C4D A:HEM501 3.1 34.7 1.0
N10 A:OY4502 3.1 52.4 1.0
C1D A:HEM501 3.1 31.3 1.0
C4C A:HEM501 3.1 35.9 1.0
C1B A:HEM501 3.1 31.8 1.0
CD2 A:HIS346 3.1 28.4 1.0
C1C A:HEM501 3.1 37.1 1.0
C4B A:HEM501 3.2 33.1 1.0
CE1 A:HIS346 3.3 28.3 1.0
N8 A:OY4502 3.4 48.9 1.0
CHA A:HEM501 3.4 35.5 1.0
CHB A:HEM501 3.4 33.0 1.0
CHD A:HEM501 3.4 36.4 1.0
C9 A:OY4502 3.5 53.3 1.0
CHC A:HEM501 3.5 36.4 1.0
C2A A:HEM501 4.2 32.2 1.0
C3A A:HEM501 4.2 29.4 1.0
CG A:HIS346 4.3 29.6 1.0
C3D A:HEM501 4.3 31.9 1.0
C2D A:HEM501 4.3 35.3 1.0
ND1 A:HIS346 4.3 24.2 1.0
C3C A:HEM501 4.3 36.3 1.0
C2B A:HEM501 4.3 34.8 1.0
C2C A:HEM501 4.3 36.6 1.0
CB A:ALA264 4.4 36.3 1.0
C3B A:HEM501 4.4 35.0 1.0
C7 A:OY4502 4.7 46.8 1.0
C12 A:OY4502 4.7 56.9 1.0
N A:ALA264 5.0 36.4 1.0

Iron binding site 2 out of 2 in 6pu7

Go back to Iron Binding Sites List in 6pu7
Iron binding site 2 out of 2 in the Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide)


Mono view


Stereo pair view

A full contact list of Iron with other atoms in the Fe binding site number 2 of Human IDO1 in Complex with Compound 17 (N-{2-[(4-{N-[(7S)-4- Fluorobicyclo[4.2.0]Octa-1,3,5-Trien-7-Yl]-N'-Hydroxycarbamimidoyl}- 1,2,5-Oxadiazol-3-Yl)Sulfanyl]Ethyl}Acetamide) within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Fe501

b:39.1
occ:1.00
 FE B:HEM501 0.0 39.1 1.0
NA B:HEM501 2.0 36.0 1.0
NC B:HEM501 2.0 32.0 1.0
NB B:HEM501 2.1 34.7 1.0
ND B:HEM501 2.1 35.0 1.0
NE2 B:HIS346 2.2 39.1 1.0
O11 B:OY4502 2.4 47.3 1.0
C4A B:HEM501 3.0 36.2 1.0
N10 B:OY4502 3.0 48.9 1.0
C1B B:HEM501 3.0 31.1 1.0
C4C B:HEM501 3.1 34.6 1.0
C1C B:HEM501 3.1 34.4 1.0
C1A B:HEM501 3.1 39.2 1.0
C1D B:HEM501 3.1 37.1 1.0
C4B B:HEM501 3.1 34.5 1.0
CD2 B:HIS346 3.1 35.2 1.0
C4D B:HEM501 3.1 36.5 1.0
CE1 B:HIS346 3.2 40.8 1.0
N8 B:OY4502 3.3 49.7 1.0
CHB B:HEM501 3.4 34.9 1.0
C9 B:OY4502 3.4 50.2 1.0
CHD B:HEM501 3.4 36.1 1.0
CHC B:HEM501 3.5 34.8 1.0
CHA B:HEM501 3.5 37.5 1.0
C3A B:HEM501 4.2 36.0 1.0
C2A B:HEM501 4.3 37.2 1.0
CG B:HIS346 4.3 37.9 1.0
C3C B:HEM501 4.3 36.7 1.0
C2B B:HEM501 4.3 33.3 1.0
C2C B:HEM501 4.3 34.2 1.0
ND1 B:HIS346 4.3 38.9 1.0
C3B B:HEM501 4.3 32.5 1.0
C2D B:HEM501 4.3 39.4 1.0
CB B:ALA264 4.3 38.8 1.0
C3D B:HEM501 4.4 35.5 1.0
C12 B:OY4502 4.6 53.5 1.0
C7 B:OY4502 4.6 54.3 1.0

Reference:

H.Zhang, K.Liu, Q.Pu, A.Achab, M.J.Ardolino, M.Cheng, Y.Deng, A.C.Doty, H.Ferguson, X.Fradera, I.Knemeyer, R.Kurukulasuriya, Y.H.Lam, C.A.Lesburg, T.A.Martinot, M.A.Mcgowan, J.R.Miller, K.Otte, P.J.Biju, N.Sciammetta, N.Solban, W.Yu, H.Zhou, X.Wang, D.J.Bennett, Y.Han. Discovery of Amino-Cyclobutarene-Derived Indoleamine-2,3-Dioxygenase 1 (IDO1) Inhibitors For Cancer Immunotherapy. Acs Med.Chem.Lett. V. 10 1530 2019.
ISSN: ISSN 1948-5875
PubMed: 31749906
DOI: 10.1021/ACSMEDCHEMLETT.9B00344
Page generated: Wed Aug 7 06:44:39 2024

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