Fluorine in PDB 5tpa: Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 9 (GNE3500)

Protein crystallography data

The structure of Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 9 (GNE3500), PDB code: 5tpa 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) 72.69 / 2.48
Space group P 21 21 21
Cell size a, b, c (Å), α, β, γ (°) 55.757, 90.239, 122.658, 90.00, 90.00, 90.00
R / Rfree (%) 18.7 / 24.1

Other elements in 5tpa:

The structure of Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 9 (GNE3500) also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Fluorine Binding Sites:

The binding sites of Fluorine atom in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 9 (GNE3500) (pdb code 5tpa). This binding sites where shown within 5.0 Angstroms radius around Fluorine atom.
In total 3 binding sites of Fluorine where determined in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 9 (GNE3500), PDB code: 5tpa:
Jump to Fluorine binding site number: 1; 2; 3;

Fluorine binding site 1 out of 3 in 5tpa

Go back to Fluorine Binding Sites List in 5tpa
Fluorine binding site 1 out of 3 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 9 (GNE3500)


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 Compound 9 (GNE3500) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:57.7
occ:1.00
F25 A:7H2302 0.0 57.7 1.0
C24 A:7H2302 1.3 51.8 1.0
F27 A:7H2302 2.1 52.9 1.0
F26 A:7H2302 2.2 50.3 1.0
C22 A:7H2302 2.3 44.1 1.0
C21 A:7H2302 2.8 44.7 1.0
CD2 B:LEU270 3.1 45.0 1.0
N23 A:7H2302 3.5 39.6 1.0
CB B:LYS140 3.7 34.4 1.0
O B:PRO141 3.8 39.5 1.0
CD B:LYS140 4.0 44.6 1.0
C20 A:7H2302 4.1 47.3 1.0
CG B:LYS140 4.2 38.9 1.0
CD2 B:HIS273 4.2 45.6 1.0
CD B:PRO141 4.2 32.4 1.0
N B:PRO141 4.3 32.0 1.0
N19 A:7H2302 4.4 40.2 1.0
NE2 B:HIS273 4.4 45.3 1.0
C B:LYS140 4.5 36.1 1.0
CA B:LYS140 4.6 32.6 1.0
CG B:LEU270 4.6 41.5 1.0
CG B:PRO141 4.7 36.6 1.0
OG1 A:THR242 4.7 33.3 1.0
CG2 A:ILE116 4.8 36.5 1.0
C B:PRO141 4.8 39.1 1.0
CA A:THR242 4.9 35.8 1.0
CG2 B:ILE269 4.9 38.2 1.0

Fluorine binding site 2 out of 3 in 5tpa

Go back to Fluorine Binding Sites List in 5tpa
Fluorine binding site 2 out of 3 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 9 (GNE3500)


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 Compound 9 (GNE3500) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:50.3
occ:1.00
F26 A:7H2302 0.0 50.3 1.0
C24 A:7H2302 1.3 51.8 1.0
F27 A:7H2302 2.1 52.9 1.0
F25 A:7H2302 2.2 57.7 1.0
C22 A:7H2302 2.4 44.1 1.0
OG1 A:THR242 2.7 33.3 1.0
N23 A:7H2302 3.1 39.6 1.0
CA A:THR242 3.4 35.8 1.0
N A:GLY243 3.4 29.4 1.0
C21 A:7H2302 3.4 44.7 1.0
CB A:THR242 3.5 39.4 1.0
CD2 B:LEU270 3.6 45.0 1.0
CG2 A:ILE116 3.7 36.5 1.0
C A:THR242 3.7 34.8 1.0
CB A:ILE116 3.7 36.8 1.0
O A:ILE116 4.2 37.7 1.0
N19 A:7H2302 4.3 40.2 1.0
CD1 A:ILE116 4.3 36.1 1.0
C20 A:7H2302 4.4 47.3 1.0
CA A:GLY243 4.5 29.2 1.0
CG1 A:ILE116 4.6 36.4 1.0
N A:THR242 4.7 37.5 1.0
C A:ILE116 4.8 36.4 1.0
O A:THR242 4.8 33.2 1.0
CA A:ILE116 4.8 33.9 1.0
CD B:LYS140 4.8 44.6 1.0
O A:GLY243 4.8 35.3 1.0
CG2 A:THR242 4.9 34.6 1.0
O A:THR241 4.9 43.0 1.0

Fluorine binding site 3 out of 3 in 5tpa

Go back to Fluorine Binding Sites List in 5tpa
Fluorine binding site 3 out of 3 in the Structure of the Human GLUN1/GLUN2A Lbd in Complex with Compound 9 (GNE3500)


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 Compound 9 (GNE3500) within 5.0Å range:
probe atom residue distance (Å) B Occ
A:F302

b:52.9
occ:1.00
F27 A:7H2302 0.0 52.9 1.0
C24 A:7H2302 1.3 51.8 1.0
F25 A:7H2302 2.1 57.7 1.0
F26 A:7H2302 2.1 50.3 1.0
C22 A:7H2302 2.3 44.1 1.0
N23 A:7H2302 2.8 39.6 1.0
CG A:PRO129 3.4 43.9 1.0
CD B:LYS140 3.4 44.6 1.0
C21 A:7H2302 3.5 44.7 1.0
CB A:PRO129 3.6 39.0 1.0
CD A:PRO129 3.7 39.1 1.0
CD1 A:ILE116 3.7 36.1 1.0
CD B:PRO141 4.0 32.4 1.0
N19 A:7H2302 4.0 40.2 1.0
CE B:LYS140 4.2 37.1 1.0
CG2 A:ILE116 4.2 36.5 1.0
C20 A:7H2302 4.3 47.3 1.0
CG B:LYS140 4.4 38.9 1.0
N A:GLY243 4.4 29.4 1.0
CB B:LYS140 4.4 34.4 1.0
CB A:ILE116 4.4 36.8 1.0
CG B:PRO141 4.4 36.6 1.0
CD2 B:LEU270 4.5 45.0 1.0
N A:PRO129 4.6 38.5 1.0
CA A:PRO129 4.6 36.9 1.0
OG1 A:THR242 4.6 33.3 1.0
CG1 A:ILE116 4.6 36.4 1.0
N B:PRO141 4.8 32.0 1.0
C A:THR242 4.8 34.8 1.0
CA A:GLY243 4.9 29.2 1.0
CA A:THR242 4.9 35.8 1.0

Reference:

E.Villemure, M.Volgraf, Y.Jiang, G.Wu, C.Q.Ly, P.W.Yuen, A.Lu, X.Luo, M.Liu, S.Zhang, P.J.Lupardus, H.J.Wallweber, B.M.Liederer, G.Deshmukh, E.Plise, S.Tay, T.M.Wang, J.E.Hanson, D.H.Hackos, K.Scearce-Levie, J.B.Schwarz, B.D.Sellers. GLUN2A-Selective Pyridopyrimidinone Series of Nmdar Positive Allosteric Modulators with An Improved in Vivo Profile. Acs Med Chem Lett V. 8 84 2017.
ISSN: ISSN 1948-5875
PubMed: 28105280
DOI: 10.1021/ACSMEDCHEMLETT.6B00388
Page generated: Sun Dec 13 12:38:22 2020

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