Fluorine in PDB 6oko: Crystal Structure of MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide

Enzymatic activity of Crystal Structure of MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide

All present enzymatic activity of Crystal Structure of MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide:
2.7.11.1;

Protein crystallography data

The structure of Crystal Structure of MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide, PDB code: 6oko was solved by M.E.Pokross, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 39.26 / 2.10
Space group C 1 2 1
Cell size a, b, c (Å), α, β, γ (°) 144.760, 52.750, 103.750, 90.00, 130.82, 90.00
R / Rfree (%) 18 / 19.8

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Crystal Structure of MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide (pdb code 6oko). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Crystal Structure of MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide, PDB code: 6oko:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 6oko

Go back to Fluorine Binding Sites List in 6oko
Fluorine binding site 1 out of 4 in the Crystal Structure of MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide


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 MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:43.8
occ:1.00
 F14 A:1FN4000 0.0 43.8 1.0
C13 A:1FN4000 1.4 41.7 1.0
C8 A:1FN4000 2.3 40.4 1.0
C12 A:1FN4000 2.3 40.6 1.0
H12 A:1FN4000 2.6 41.0 0.0
O7 A:1FN4000 2.7 40.0 1.0
H5 A:1FN4000 3.3 33.2 0.0
CB A:ALA49 3.5 32.5 1.0
C6 A:1FN4000 3.5 36.6 1.0
CB A:LYS51 3.5 38.5 1.0
CG1 A:VAL36 3.6 37.0 1.0
C9 A:1FN4000 3.6 37.9 1.0
C11 A:1FN4000 3.6 38.2 1.0
C5 A:1FN4000 3.7 33.2 1.0
CG2 A:VAL36 3.8 38.5 1.0
C10 A:1FN4000 4.1 37.6 1.0
N A:LYS51 4.2 37.4 1.0
CB A:VAL36 4.3 38.4 1.0
CA A:LYS51 4.4 37.2 1.0
C A:ALA49 4.4 37.9 1.0
CG A:LYS51 4.4 42.7 1.0
CD A:LYS51 4.4 46.0 1.0
H9 A:1FN4000 4.5 37.6 0.0
OG1 A:THR95 4.5 40.0 1.0
CA A:ALA49 4.5 33.0 1.0
N A:VAL50 4.6 34.1 1.0
C A:VAL50 4.7 41.3 1.0
O A:ALA49 4.7 38.1 1.0
C1 A:1FN4000 4.7 39.7 1.0
N15 A:1FN4000 4.8 37.0 1.0
O19 A:1FN4000 5.0 44.6 1.0

Fluorine binding site 2 out of 4 in 6oko

Go back to Fluorine Binding Sites List in 6oko
Fluorine binding site 2 out of 4 in the Crystal Structure of MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide


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 MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F4000

b:49.0
occ:1.00
 F35 A:1FN4000 0.0 49.0 1.0
C32 A:1FN4000 1.4 42.9 1.0
C33 A:1FN4000 2.3 42.0 1.0
C31 A:1FN4000 2.3 42.2 1.0
H31 A:1FN4000 2.6 41.7 0.0
H33 A:1FN4000 2.6 42.1 0.0
CD1 A:LEU132 3.1 36.9 1.0
CD2 A:HIS141 3.5 38.5 1.0
C34 A:1FN4000 3.6 42.7 1.0
C30 A:1FN4000 3.6 41.4 1.0
CD2 A:LEU132 3.8 34.0 1.0
CB A:LEU159 4.0 31.6 1.0
CG A:LEU132 4.0 36.6 1.0
C26 A:1FN4000 4.1 40.6 1.0
NE2 A:HIS141 4.1 38.6 1.0
CG1 A:VAL73 4.2 33.6 1.0
O A:LEU159 4.2 32.2 1.0
C A:LEU159 4.3 34.4 1.0
CD1 A:LEU68 4.5 36.7 1.0
H30 A:1FN4000 4.5 41.3 0.0
H34 A:1FN4000 4.5 43.1 0.0
N A:ALA160 4.5 32.9 1.0
CG A:HIS141 4.6 37.8 1.0
CA A:ALA160 4.8 34.4 1.0
CA A:LEU159 4.8 31.7 1.0
CD2 A:LEU139 4.9 53.2 1.0
CG2 A:VAL73 4.9 33.1 1.0
CD1 A:LEU159 4.9 36.7 1.0
C A:ALA160 5.0 38.4 1.0

Fluorine binding site 3 out of 4 in 6oko

Go back to Fluorine Binding Sites List in 6oko
Fluorine binding site 3 out of 4 in the Crystal Structure of MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide


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 MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F4000

b:60.2
occ:1.00
 F14 B:1FN4000 0.0 60.2 1.0
C13 B:1FN4000 1.4 57.2 1.0
C12 B:1FN4000 2.3 57.2 1.0
C8 B:1FN4000 2.3 53.3 1.0
H12 B:1FN4000 2.6 57.5 0.0
O7 B:1FN4000 2.7 48.7 1.0
H5 B:1FN4000 3.2 43.8 0.0
CG1 B:VAL36 3.4 52.4 1.0
C6 B:1FN4000 3.5 44.8 1.0
CB B:ALA49 3.5 42.1 1.0
C11 B:1FN4000 3.6 57.5 1.0
C9 B:1FN4000 3.6 52.5 1.0
CB B:LYS51 3.6 49.2 1.0
C5 B:1FN4000 3.6 43.9 1.0
CG2 B:VAL36 3.8 55.3 1.0
C10 B:1FN4000 4.1 54.1 1.0
CB B:VAL36 4.2 55.0 1.0
CG B:LYS51 4.2 62.6 1.0
N B:LYS51 4.4 46.1 1.0
C B:ALA49 4.4 44.0 1.0
CA B:LYS51 4.5 47.6 1.0
H9 B:1FN4000 4.5 52.6 0.0
OG1 B:THR95 4.5 41.3 1.0
CA B:ALA49 4.5 41.7 1.0
N B:VAL50 4.6 41.7 1.0
C1 B:1FN4000 4.7 45.7 1.0
C B:VAL50 4.7 49.2 1.0
O B:ALA49 4.7 42.1 1.0
N15 B:1FN4000 4.8 59.6 1.0
C4 B:1FN4000 4.9 44.7 1.0
CD B:LYS51 5.0 69.7 1.0

Fluorine binding site 4 out of 4 in 6oko

Go back to Fluorine Binding Sites List in 6oko
Fluorine binding site 4 out of 4 in the Crystal Structure of MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide


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 MRIPK3 Complexed with N-(3-Fluoro-4-{1H- Pyrrolo[2,3-B]Pyridin-4-Yloxy}Phenyl)-1-(4-Fluorophenyl)-2-Oxo-1,2- Dihydropyridine-3-Carboxamide within 5.0Å range:
probe atom residue distance (Å) B Occ
B:F4000

b:65.9
occ:1.00
 F35 B:1FN4000 0.0 65.9 1.0
C32 B:1FN4000 1.4 61.6 1.0
C31 B:1FN4000 2.3 58.5 1.0
C33 B:1FN4000 2.3 60.9 1.0
H31 B:1FN4000 2.6 57.5 0.0
H33 B:1FN4000 2.6 62.2 0.0
CD1 B:LEU132 3.2 50.4 1.0
CD2 B:HIS141 3.3 63.8 1.0
C30 B:1FN4000 3.6 57.2 1.0
C34 B:1FN4000 3.6 60.0 1.0
NE2 B:HIS141 3.9 63.0 1.0
CB B:LEU159 3.9 47.8 1.0
CD2 B:LEU132 4.0 50.6 1.0
C26 B:1FN4000 4.1 58.7 1.0
O B:LEU159 4.1 46.8 1.0
C B:LEU159 4.2 49.3 1.0
CG B:LEU132 4.2 50.2 1.0
CG1 B:VAL73 4.4 46.1 1.0
CG B:HIS141 4.4 64.1 1.0
N B:ALA160 4.4 48.6 1.0
H30 B:1FN4000 4.5 56.4 0.0
H34 B:1FN4000 4.5 61.5 0.0
CG B:LEU159 4.7 54.9 1.0
CD1 B:LEU68 4.7 47.8 1.0
CA B:ALA160 4.7 49.4 1.0
CA B:LEU159 4.7 46.2 1.0
CD2 B:LEU159 4.8 56.1 1.0
C B:ALA160 4.9 55.8 1.0
O B:ALA160 5.0 55.7 1.0
CD2 B:LEU139 5.0 68.2 1.0

Reference:

A.C.Hart, L.Abell, J.Guo, M.E.Mertzman, R.Padmanabha, J.E.Macor, C.Chaudhry, H.Lu, K.O'malley, P.J.Shaw, C.Weigelt, M.E.Pokross, K.Kish, K.S.Kim, L.Cornelius, A.E.Douglas, D.Calambur, P.Zhang, B.Carpenter, W.J.Pitts. Identification of RIPK3 Type II Inhibitors Using High-Throughput Mechanistic Studies in Hit Triage Acs Med.Chem.Lett. 2019.
ISSN: ISSN 1948-5875
DOI: 10.1021/ACSMEDCHEMLETT.9B00065
Page generated: Sun Dec 13 13:02:24 2020

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