Sodium in PDB 7t78: Crystal Structure of Glucokinase (Hexokinase 4) Complexed with Ligand Diethyl ({2-[3-(4-Methanesulfonylpheno Xy)-5-{[(2S)-1-Methoxypropan- 2-Yl]Oxy}Benzamido]-1,3-Thiaz Ol-4-Yl}Methyl)Phosphonate

Enzymatic activity of Crystal Structure of Glucokinase (Hexokinase 4) Complexed with Ligand Diethyl ({2-[3-(4-Methanesulfonylpheno Xy)-5-{[(2S)-1-Methoxypropan- 2-Yl]Oxy}Benzamido]-1,3-Thiaz Ol-4-Yl}Methyl)Phosphonate

All present enzymatic activity of Crystal Structure of Glucokinase (Hexokinase 4) Complexed with Ligand Diethyl ({2-[3-(4-Methanesulfonylpheno Xy)-5-{[(2S)-1-Methoxypropan- 2-Yl]Oxy}Benzamido]-1,3-Thiaz Ol-4-Yl}Methyl)Phosphonate:
2.7.1.1;

Protein crystallography data

The structure of Crystal Structure of Glucokinase (Hexokinase 4) Complexed with Ligand Diethyl ({2-[3-(4-Methanesulfonylpheno Xy)-5-{[(2S)-1-Methoxypropan- 2-Yl]Oxy}Benzamido]-1,3-Thiaz Ol-4-Yl}Methyl)Phosphonate, PDB code: 7t78 was solved by J.K.Muckelbauer, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 43.83 / 2.40
Space group P 1 21 1
Cell size a, b, c (Å), α, β, γ (°) 76.37, 83.7, 84.97, 90, 100.38, 90
R / Rfree (%) 18.5 / 22.2

Sodium Binding Sites:

The binding sites of Sodium atom in the Crystal Structure of Glucokinase (Hexokinase 4) Complexed with Ligand Diethyl ({2-[3-(4-Methanesulfonylpheno Xy)-5-{[(2S)-1-Methoxypropan- 2-Yl]Oxy}Benzamido]-1,3-Thiaz Ol-4-Yl}Methyl)Phosphonate (pdb code 7t78). This binding sites where shown within 5.0 Angstroms radius around Sodium atom.
In total 2 binding sites of Sodium where determined in the Crystal Structure of Glucokinase (Hexokinase 4) Complexed with Ligand Diethyl ({2-[3-(4-Methanesulfonylpheno Xy)-5-{[(2S)-1-Methoxypropan- 2-Yl]Oxy}Benzamido]-1,3-Thiaz Ol-4-Yl}Methyl)Phosphonate, PDB code: 7t78:
Jump to Sodium binding site number: 1; 2;

Sodium binding site 1 out of 2 in 7t78

Go back to Sodium Binding Sites List in 7t78
Sodium binding site 1 out of 2 in the Crystal Structure of Glucokinase (Hexokinase 4) Complexed with Ligand Diethyl ({2-[3-(4-Methanesulfonylpheno Xy)-5-{[(2S)-1-Methoxypropan- 2-Yl]Oxy}Benzamido]-1,3-Thiaz Ol-4-Yl}Methyl)Phosphonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 1 of Crystal Structure of Glucokinase (Hexokinase 4) Complexed with Ligand Diethyl ({2-[3-(4-Methanesulfonylpheno Xy)-5-{[(2S)-1-Methoxypropan- 2-Yl]Oxy}Benzamido]-1,3-Thiaz Ol-4-Yl}Methyl)Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Na502

b:75.7
occ:1.00
 O A:VAL241 2.2 60.6 1.0
O A:MET238 2.2 60.5 1.0
O A:VAL244 2.3 58.3 1.0
O A:GLY246 2.5 68.8 1.0
C A:VAL241 3.3 59.7 1.0
C A:MET238 3.4 60.8 1.0
C A:VAL244 3.5 60.3 1.0
C A:GLY246 3.7 67.6 1.0
N A:GLY246 3.8 62.4 1.0
CE A:MET238 4.0 57.5 1.0
CA A:VAL241 4.2 55.5 1.0
N A:GLU242 4.2 53.9 1.0
N A:GLN239 4.2 60.1 1.0
CA A:GLN239 4.2 61.0 1.0
C A:GLU245 4.2 65.4 1.0
CA A:GLY246 4.3 62.6 1.0
CB A:VAL241 4.3 58.2 1.0
N A:VAL241 4.3 56.2 1.0
CA A:GLU242 4.3 52.8 1.0
CA A:MET238 4.4 53.8 1.0
N A:GLU245 4.4 60.4 1.0
C A:GLN239 4.4 66.3 1.0
CA A:GLU245 4.4 60.6 1.0
O A:GLN239 4.4 67.2 1.0
N A:VAL244 4.5 52.5 1.0
CA A:VAL244 4.5 53.8 1.0
CB A:MET238 4.6 55.4 1.0
C A:GLU242 4.7 56.8 1.0
N A:ASP247 4.7 64.0 1.0
SD A:MET238 4.8 61.1 1.0
O A:GLU245 4.9 65.5 1.0
CG1 A:VAL241 5.0 57.8 1.0
CB A:VAL244 5.0 57.3 1.0

Sodium binding site 2 out of 2 in 7t78

Go back to Sodium Binding Sites List in 7t78
Sodium binding site 2 out of 2 in the Crystal Structure of Glucokinase (Hexokinase 4) Complexed with Ligand Diethyl ({2-[3-(4-Methanesulfonylpheno Xy)-5-{[(2S)-1-Methoxypropan- 2-Yl]Oxy}Benzamido]-1,3-Thiaz Ol-4-Yl}Methyl)Phosphonate


Mono view


Stereo pair view

A full contact list of Sodium with other atoms in the Na binding site number 2 of Crystal Structure of Glucokinase (Hexokinase 4) Complexed with Ligand Diethyl ({2-[3-(4-Methanesulfonylpheno Xy)-5-{[(2S)-1-Methoxypropan- 2-Yl]Oxy}Benzamido]-1,3-Thiaz Ol-4-Yl}Methyl)Phosphonate within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Na502

b:63.2
occ:1.00
 O B:MET238 2.3 44.0 1.0
O B:VAL244 2.3 45.9 1.0
O B:VAL241 2.3 43.3 1.0
O B:GLY246 2.4 46.0 1.0
C B:VAL241 3.4 43.8 1.0
C B:MET238 3.4 44.0 1.0
C B:VAL244 3.5 45.4 1.0
C B:GLY246 3.5 45.6 1.0
N B:GLY246 3.7 38.8 1.0
CE B:MET238 4.0 41.9 1.0
C B:GLU245 4.1 43.2 1.0
CA B:GLY246 4.2 38.9 1.0
N B:GLN239 4.2 41.8 1.0
CA B:GLN239 4.2 41.1 1.0
N B:GLU242 4.3 40.0 1.0
CA B:VAL241 4.3 38.4 1.0
OD1 B:ASP247 4.3 61.2 1.0
CA B:GLU245 4.3 42.8 1.0
N B:GLU245 4.4 42.5 1.0
CA B:GLU242 4.4 40.1 1.0
CA B:MET238 4.4 37.0 1.0
N B:VAL241 4.4 39.1 1.0
CB B:VAL241 4.4 40.9 1.0
C B:GLN239 4.4 43.8 1.0
O B:GLN239 4.5 43.4 1.0
N B:VAL244 4.6 38.6 1.0
CA B:VAL244 4.6 38.4 1.0
CB B:MET238 4.6 39.0 1.0
N B:ASP247 4.7 44.5 1.0
C B:GLU242 4.8 42.5 1.0
O B:GLU245 4.8 41.7 1.0
SD B:MET238 4.9 44.7 1.0
CA B:ASP247 5.0 45.4 1.0

Reference:

Y.Shi, Y.Wang, W.Meng, R.P.Brigance, D.E.Ryono, S.Bolton, H.Zhang, S.Chen, R.Smirk, S.Tao, J.A.Tino, K.N.Williams, R.Sulsky, L.Nielsen, B.Ellsworth, M.K.Y.Wong, J.H.Sun, L.W.Leith, D.Sun, D.R.Wu, A.Gupta, R.Rampulla, A.Mathur, B.C.Chen, A.Wang, H.G.Fuentes-Catanio, L.Kunselman, M.Cap, J.Zalaznick, X.Ma, H.Liu, J.R.Taylor, R.Zebo, B.Jones, S.Kalinowski, J.Swartz, A.Staal, K.O'malley, L.Kopcho, J.K.Muckelbauer, S.R.Krystek Jr., S.A.Spronk, J.Marcinkeviciene, G.Everlof, X.Q.Chen, C.Xu, Y.X.Li, R.A.Langish, Y.Yang, Q.Wang, K.Behnia, A.Fura, E.B.Janovitz, N.Pannacciulli, S.Griffen, B.A.Zinker, J.Krupinski, M.Kirby, J.Whaley, R.Zahler, J.C.Barrish, J.A.Robl, P.T.W.Cheng. Discovery of A Partial Glucokinase Activator Clinical Candidate: Diethyl ((3-(3-((5-(Azetidine-1-Carbonyl)Pyrazin-2-Yl)Oxy) -5-Isopropoxybenzamido)-1 H -Pyrazol-1-Yl)Methyl)Phosphonate (Bms-820132). J.Med.Chem. V. 65 4291 2022.
ISSN: ISSN 0022-2623
PubMed: 35179904
DOI: 10.1021/ACS.JMEDCHEM.1C02110
Page generated: Wed Oct 9 09:05:10 2024

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