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Fluorine in PDB 5i2n: Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29)

Protein crystallography data

The structure of Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29), PDB code: 5i2n was solved by H.J.A.Wallweber, P.J.Lupardus, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 72.10 / 2.12
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 56.521, 89.859, 120.801, 90.00, 90.00, 90.00
R / Rfree (%) 18.6 / 22.3

Other elements in 5i2n:

The structure of Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29) also contains other interesting chemical elements:

Calcium (Ca) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29) (pdb code 5i2n). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 4 binding sites of Fluorine where determined in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29), PDB code: 5i2n:
Jump to Fluorine binding site number: 1; 2; 3; 4;

Fluorine binding site 1 out of 4 in 5i2n

Go back to Fluorine Binding Sites List in 5i2n
Fluorine binding site 1 out of 4 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 1 of Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:28.6
occ:1.00
F23 A:67J303 0.0 28.6 1.0
C22 A:67J303 1.3 26.9 1.0
C17 A:67J303 2.3 28.3 1.0
C21 A:67J303 2.3 29.1 1.0
F27 A:67J303 2.7 35.3 1.0
C24 A:67J303 2.8 34.9 1.0
C16 A:67J303 2.8 27.6 1.0
F26 A:67J303 2.9 39.5 1.0
C14 A:67J303 3.0 30.2 1.0
CB A:PRO129 3.1 23.6 1.0
N A:GLY243 3.1 22.8 1.0
C A:THR242 3.2 26.0 1.0
CG A:PRO129 3.2 27.6 1.0
O A:THR242 3.3 26.4 1.0
C13 A:67J303 3.4 27.8 1.0
CA A:GLY243 3.4 22.1 1.0
C18 A:67J303 3.6 26.4 1.0
C20 A:67J303 3.6 30.1 1.0
N15 A:67J303 3.8 31.4 1.0
CA A:THR242 3.9 24.8 1.0
C19 A:67J303 4.1 27.4 1.0
F25 A:67J303 4.1 33.6 1.0
C11 A:67J303 4.4 26.5 1.0
CD A:PRO129 4.4 24.1 1.0
CG B:PRO141 4.5 26.9 1.0
C A:GLY243 4.6 24.4 1.0
CA A:PRO129 4.6 23.0 1.0
C9 A:67J303 4.7 29.8 1.0
OG1 A:THR242 4.8 21.9 1.0
N A:THR242 4.8 27.2 1.0
CD1 A:ILE116 4.9 24.1 1.0
CD B:PRO141 5.0 22.5 1.0
N10 A:67J303 5.0 26.6 1.0

Fluorine binding site 2 out of 4 in 5i2n

Go back to Fluorine Binding Sites List in 5i2n
Fluorine binding site 2 out of 4 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 2 of Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:33.6
occ:1.00
F25 A:67J303 0.0 33.6 1.0
C24 A:67J303 1.3 34.9 1.0
F27 A:67J303 2.1 35.3 1.0
F26 A:67J303 2.2 39.5 1.0
C21 A:67J303 2.4 29.1 1.0
C20 A:67J303 2.7 30.1 1.0
O A:HOH521 3.2 45.1 1.0
CD2 B:LEU270 3.3 23.1 1.0
C22 A:67J303 3.6 26.9 1.0
CB B:LYS140 3.7 23.8 1.0
O B:PRO141 3.7 27.2 1.0
CD2 B:HIS273 4.0 22.8 1.0
F23 A:67J303 4.1 28.6 1.0
CD B:PRO141 4.1 22.5 1.0
C19 A:67J303 4.1 27.4 1.0
N B:PRO141 4.2 21.9 1.0
NE2 B:HIS273 4.3 22.8 1.0
CG B:LYS140 4.4 22.3 1.0
CD B:LYS140 4.4 23.9 1.0
C B:LYS140 4.4 25.0 1.0
CG B:PRO141 4.5 26.9 1.0
CA B:LYS140 4.6 21.5 1.0
CG B:LEU270 4.6 23.2 1.0
OG1 A:THR242 4.6 21.9 1.0
C B:PRO141 4.7 26.8 1.0
C17 A:67J303 4.8 28.3 1.0
CA B:PRO141 4.9 21.6 1.0
CA A:THR242 4.9 24.8 1.0
CG2 B:ILE269 4.9 22.2 1.0
C18 A:67J303 5.0 26.4 1.0
CG B:HIS273 5.0 22.8 1.0

Fluorine binding site 3 out of 4 in 5i2n

Go back to Fluorine Binding Sites List in 5i2n
Fluorine binding site 3 out of 4 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 3 of Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:39.5
occ:1.00
F26 A:67J303 0.0 39.5 1.0
C24 A:67J303 1.4 34.9 1.0
F27 A:67J303 2.1 35.3 1.0
F25 A:67J303 2.2 33.6 1.0
C21 A:67J303 2.4 29.1 1.0
OG1 A:THR242 2.9 21.9 1.0
F23 A:67J303 2.9 28.6 1.0
C22 A:67J303 3.0 26.9 1.0
O A:HOH521 3.3 45.1 1.0
N A:GLY243 3.3 22.8 1.0
CA A:THR242 3.4 24.8 1.0
C20 A:67J303 3.5 30.1 1.0
C A:THR242 3.6 26.0 1.0
CB A:THR242 3.7 26.3 1.0
CD2 B:LEU270 4.0 23.1 1.0
CD1 A:ILE116 4.1 24.1 1.0
CG2 A:ILE116 4.1 24.1 1.0
CB A:ILE116 4.1 23.8 1.0
CA A:GLY243 4.3 22.1 1.0
C17 A:67J303 4.4 28.3 1.0
O A:THR242 4.5 26.4 1.0
C19 A:67J303 4.7 27.4 1.0
N A:THR242 4.7 27.2 1.0
O A:GLY243 4.7 23.4 1.0
CG1 A:ILE116 4.8 23.3 1.0
CB A:PRO129 4.8 23.6 1.0
O A:THR241 4.9 33.2 1.0
CD B:LYS140 4.9 23.9 1.0
O A:ILE116 4.9 20.1 1.0
CG A:PRO129 4.9 27.6 1.0
C A:GLY243 5.0 24.4 1.0

Fluorine binding site 4 out of 4 in 5i2n

Go back to Fluorine Binding Sites List in 5i2n
Fluorine binding site 4 out of 4 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29)


Mono view


Stereo pair view

A full contact list of Fluorine with other atoms in the F binding site number 4 of Structure of the Human GLUN1/GLUN2A Lbd in Complex with N-Ethyl-7-{[2- Fluoro-3-(Trifluoromethyl)Phenyl]Methyl}-2-Methyl-5-Oxo-5H-[1, 3]Thiazolo[3,2-A]Pyrimidine-3-Carboxamide (Compound 29) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F303

b:35.3
occ:1.00
F27 A:67J303 0.0 35.3 1.0
C24 A:67J303 1.3 34.9 1.0
F26 A:67J303 2.1 39.5 1.0
F25 A:67J303 2.1 33.6 1.0
C21 A:67J303 2.3 29.1 1.0
F23 A:67J303 2.7 28.6 1.0
C22 A:67J303 2.9 26.9 1.0
CD B:PRO141 3.3 22.5 1.0
CG A:PRO129 3.4 27.6 1.0
C20 A:67J303 3.5 30.1 1.0
CG B:PRO141 3.7 26.9 1.0
CD B:LYS140 3.7 23.9 1.0
CD A:PRO129 3.8 24.1 1.0
CB A:PRO129 3.9 23.6 1.0
CB B:LYS140 4.1 23.8 1.0
N B:PRO141 4.1 21.9 1.0
C17 A:67J303 4.2 28.3 1.0
CD1 A:ILE116 4.3 24.1 1.0
CG B:LYS140 4.4 22.3 1.0
CA B:LYS140 4.6 21.5 1.0
C19 A:67J303 4.6 27.4 1.0
C B:LYS140 4.7 25.0 1.0
N A:GLY243 4.7 22.8 1.0
CD2 B:LEU270 4.7 23.1 1.0
O B:PRO141 4.8 27.2 1.0
CE B:LYS140 4.8 21.7 1.0
O A:HOH521 4.8 45.1 1.0
N A:PRO129 4.9 23.2 1.0
CB B:PRO141 4.9 23.3 1.0
C18 A:67J303 4.9 26.4 1.0
OG1 A:THR242 4.9 21.9 1.0
C A:THR242 5.0 26.0 1.0
CG2 A:ILE116 5.0 24.1 1.0

Reference:

M.Volgraf, B.D.Sellers, Y.Jiang, G.Wu, C.Q.Ly, E.Villemure, R.M.Pastor, P.W.Yuen, A.Lu, X.Luo, M.Liu, S.Zhang, L.Sun, Y.Fu, P.J.Lupardus, H.J.Wallweber, B.M.Liederer, G.Deshmukh, E.Plise, S.Tay, P.Reynen, J.Herrington, A.Gustafson, Y.Liu, A.Dirksen, M.G.Dietz, Y.Liu, T.M.Wang, J.E.Hanson, D.Hackos, K.Scearce-Levie, J.B.Schwarz. Discovery of GLUN2A-Selective Nmda Receptor Positive Allosteric Modulators (Pams): Tuning Deactivation Kinetics Via Structure-Based Design. J.Med.Chem. V. 59 2760 2016.
ISSN: ISSN 0022-2623
PubMed: 26919761
DOI: 10.1021/ACS.JMEDCHEM.5B02010
Page generated: Sun Dec 13 12:24:06 2020

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