Calcium in PDB 5g3n: Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor.

All present enzymatic activity of Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor.:
3.1.1.4;

The structure of Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor., PDB code: 5g3n was solved by J.Sandmark, C.Bodin, K.Hallberg, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	24.56 / 1.80
Space group	P 21 21 21
Cell size a, b, c (Å), α, β, γ (°)	52.100, 66.530, 73.770, 90.00, 90.00, 90.00
R / Rfree (%)	19.5 / 23.1

The binding sites of Calcium atom in the Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor. (pdb code 5g3n). This binding sites where shown within 5.0 Angstroms radius around Calcium atom.
In total 4 binding sites of Calcium where determined in the Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor., PDB code: 5g3n:
Jump to Calcium binding site number: 1; 2; 3; 4;

Calcium binding site 1 out of 4 in the Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 1 of Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca198 b:20.9 occ:1.00 O A:HIS27 2.3 21.1 1.0 O A:GLY29 2.3 26.9 1.0 OD1 A:ASP48 2.4 18.3 1.0 O26 A:X281129 2.4 16.9 1.0 OD2 A:ASP48 2.4 24.2 1.0 O23 A:X281129 2.4 28.8 1.0 O A:GLY31 2.5 28.0 1.0 CG A:ASP48 2.7 21.7 1.0 C25 A:X281129 3.5 17.6 1.0 C A:GLY29 3.5 26.1 1.0 C A:HIS27 3.5 21.1 1.0 C22 A:X281129 3.5 23.7 1.0 C A:GLY31 3.6 30.6 1.0 N A:GLY29 3.8 19.6 1.0 N A:GLY31 3.8 24.8 1.0 N27 A:X281129 3.9 16.7 1.0 CA A:GLY31 4.2 26.6 1.0 C A:VAL30 4.2 27.2 1.0 CB A:ASP48 4.2 16.4 1.0 C21 A:X281129 4.2 25.9 1.0 C A:CYS28 4.3 21.5 1.0 CA A:GLY29 4.3 19.5 1.0 CA A:CYS28 4.3 16.2 1.0 N A:CYS28 4.4 16.7 1.0 CA A:HIS27 4.4 18.6 1.0 O A:HOH2054 4.4 44.4 1.0 N A:VAL30 4.5 21.9 1.0 CA A:VAL30 4.6 22.4 1.0 O24 A:X281129 4.6 20.8 1.0 N A:GLY32 4.7 26.6 1.0 C19 A:X281129 4.7 21.1 1.0 O A:VAL30 4.7 26.7 1.0 C11 A:X281129 4.7 14.9 1.0 O A:HOH2030 4.8 23.4 1.0 O A:CYS44 4.8 14.3 1.0 CB A:HIS27 4.8 19.4 1.0 C18 A:X281129 5.0 21.5 1.0 CA A:GLY32 5.0 25.8 1.0

Calcium binding site 2 out of 4 in the Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 2 of Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ A:Ca199 b:49.6 occ:1.00 O A:PHE23 2.3 21.0 1.0 O A:HOH2028 2.3 27.1 1.0 O A:TYR112 2.3 27.2 1.0 O A:GLY25 2.5 22.8 1.0 OD1 A:ASN114 3.0 52.7 1.0 C A:PHE23 3.2 21.3 1.0 C A:TYR112 3.4 30.3 1.0 C A:GLY25 3.6 23.7 1.0 C A:TYR24 3.8 19.6 1.0 N A:TYR112 3.9 27.1 1.0 N A:GLY25 3.9 20.0 1.0 CA A:TYR112 3.9 27.0 1.0 O A:TYR24 4.0 17.7 1.0 CA A:PHE23 4.0 17.4 1.0 CB A:TYR112 4.0 28.1 1.0 N A:TYR24 4.1 17.7 1.0 CG A:ASN114 4.2 66.6 1.0 CA A:GLY25 4.3 19.6 1.0 O A:CYS28 4.4 20.6 1.0 CA A:TYR24 4.4 16.1 1.0 CB A:PHE23 4.4 18.4 1.0 N A:SER113 4.5 31.1 1.0 N A:ASN114 4.6 39.1 1.0 N A:CYS26 4.6 22.7 1.0 C A:TYR111 4.8 28.0 1.0 CA A:SER113 4.8 32.8 1.0 CA A:CYS26 4.8 22.9 1.0 C A:SER113 5.0 39.1 1.0 ND2 A:ASN114 5.0 60.6 1.0

Calcium binding site 3 out of 4 in the Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 3 of Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca198 b:18.8 occ:1.00 O B:GLY29 2.2 19.8 1.0 O24 B:X281126 2.3 26.2 1.0 O B:HIS27 2.3 20.8 1.0 OD2 B:ASP48 2.3 22.5 1.0 O B:GLY31 2.4 25.1 1.0 OD1 B:ASP48 2.4 20.1 1.0 O26 B:X281126 2.5 17.3 1.0 CG B:ASP48 2.7 19.8 1.0 C B:GLY29 3.5 20.7 1.0 C B:HIS27 3.5 18.8 1.0 C25 B:X281126 3.5 19.5 1.0 C B:GLY31 3.6 27.0 1.0 C22 B:X281126 3.6 29.1 1.0 N B:GLY29 3.8 18.1 1.0 N B:GLY31 3.9 24.6 1.0 N27 B:X281126 3.9 15.9 1.0 C21 B:X281126 4.2 27.7 1.0 O B:HOH2026 4.2 32.9 1.0 C B:VAL30 4.2 27.3 1.0 CA B:GLY31 4.2 24.9 1.0 CB B:ASP48 4.2 13.7 1.0 CA B:GLY29 4.3 17.7 1.0 C B:CYS28 4.3 20.6 1.0 N B:CYS28 4.4 14.1 1.0 CA B:HIS27 4.4 16.4 1.0 CA B:CYS28 4.4 13.7 1.0 O B:HOH2049 4.4 36.1 1.0 N B:VAL30 4.4 19.6 1.0 O23 B:X281126 4.5 29.5 1.0 CA B:VAL30 4.5 20.7 1.0 N B:GLY32 4.6 25.5 1.0 C19 B:X281126 4.7 18.7 1.0 O B:VAL30 4.8 27.5 1.0 O B:HOH2027 4.8 22.9 1.0 O B:CYS44 4.8 14.4 1.0 C11 B:X281126 4.8 14.3 1.0 CB B:HIS27 4.8 16.0 1.0 CA B:GLY32 4.9 25.5 1.0 C18 B:X281126 5.0 21.1 1.0

Calcium binding site 4 out of 4 in the Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor.


Mono view


Stereo pair view

A full contact list of Calcium with other atoms in the Ca binding site number 4 of Discovery of A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor. within 5.0Å range: probe atom residue distance (Å) B Occ B:Ca199 b:41.8 occ:1.00 O B:HOH2024 2.2 25.6 1.0 O B:TYR112 2.2 28.5 1.0 O B:PHE23 2.3 19.0 1.0 O B:GLY25 2.5 21.3 1.0 C B:PHE23 3.1 20.0 1.0 C B:TYR112 3.3 30.8 1.0 C B:GLY25 3.6 23.1 1.0 C B:TYR24 3.7 18.0 1.0 N B:TYR112 3.8 26.7 1.0 N B:GLY25 3.9 17.4 1.0 CA B:TYR112 3.9 25.6 1.0 CA B:PHE23 3.9 16.2 1.0 CB B:TYR112 3.9 26.6 1.0 O B:TYR24 4.0 18.5 1.0 N B:TYR24 4.0 15.6 1.0 CA B:TYR24 4.2 13.6 1.0 O B:CYS28 4.2 20.0 1.0 CA B:GLY25 4.3 18.2 1.0 CB B:PHE23 4.4 17.3 1.0 O B:HOH2028 4.5 31.8 1.0 N B:SER113 4.5 31.3 1.0 N B:CYS26 4.6 21.6 1.0 C B:TYR111 4.8 29.0 1.0 CA B:SER113 4.8 32.6 1.0 N B:ASN114 4.9 36.4 1.0 CA B:CYS26 4.9 21.6 1.0 C B:SER113 4.9 37.2 1.0

F.Giordanetto, D.Pettersen, I.Starke, P.Nordberg, M.Dahlstrom, L.Knerr, N.Selmi, B.Rosengren, L.O.Larsson, J.Sandmark, M.Castaldo, N.Dekker, U.Karlsson, E.Hurt-Camejo. Discovery of AZD2716: A Novel Secreted Phospholipase A2 (SPLA2) Inhibitor For the Treatment of Coronary Artery Disease Acs Med.Chem.Lett. V. 7 884 2016.
ISSN: ISSN 1948-5875
PubMed: 27774123
DOI: 10.1021/ACSMEDCHEMLETT.6B00188