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5G3M
Asym. Unit
Info
Asym.Unit (52 KB)
Biol.Unit 1 (24 KB)
Biol.Unit 2 (24 KB)
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(1)
Title
:
DISCOVERY OF A NOVEL SECRETED PHOSPHOLIPASE A2 (SPLA2) INHIBITOR.
Authors
:
J. Sandmark, C. Bodin, K. Hallberg
Date
:
29 Apr 16 (Deposition) - 14 Sep 16 (Release) - 09 Nov 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Hydrolase, Spla2, Cardiovascular Disease, Inhibitor, Fragment
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
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
[
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Hetero Components
(4, 25)
Info
All Hetero Components
1a: 4-BENZYLBENZAMIDE (9JHa)
1b: 4-BENZYLBENZAMIDE (9JHb)
2a: CALCIUM ION (CAa)
2b: CALCIUM ION (CAb)
3a: DIMETHYL SULFOXIDE (DMSa)
3b: DIMETHYL SULFOXIDE (DMSb)
3c: DIMETHYL SULFOXIDE (DMSc)
3d: DIMETHYL SULFOXIDE (DMSd)
3e: DIMETHYL SULFOXIDE (DMSe)
3f: DIMETHYL SULFOXIDE (DMSf)
3g: DIMETHYL SULFOXIDE (DMSg)
3h: DIMETHYL SULFOXIDE (DMSh)
3i: DIMETHYL SULFOXIDE (DMSi)
3j: DIMETHYL SULFOXIDE (DMSj)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
4d: DI(HYDROXYETHYL)ETHER (PEGd)
4e: DI(HYDROXYETHYL)ETHER (PEGe)
4f: DI(HYDROXYETHYL)ETHER (PEGf)
4g: DI(HYDROXYETHYL)ETHER (PEGg)
4h: DI(HYDROXYETHYL)ETHER (PEGh)
4i: DI(HYDROXYETHYL)ETHER (PEGi)
4j: DI(HYDROXYETHYL)ETHER (PEGj)
4k: DI(HYDROXYETHYL)ETHER (PEGk)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
9JH
2
Ligand/Ion
4-BENZYLBENZAMIDE
2
CA
2
Ligand/Ion
CALCIUM ION
3
DMS
10
Ligand/Ion
DIMETHYL SULFOXIDE
4
PEG
11
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
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]
Sites
(25, 25)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:26 , GLY A:28 , GLY A:30 , ASP A:47 , PEG A:1128 , 9JH A:1134
BINDING SITE FOR RESIDUE CA A 200
02
AC2
SOFTWARE
PHE B:26 , GLY B:28 , GLY B:30 , ASP B:47 , PEG B:1132 , 9JH B:1133
BINDING SITE FOR RESIDUE CA B 200
03
AC3
SOFTWARE
HIS A:44
BINDING SITE FOR RESIDUE DMS A1124
04
AC4
SOFTWARE
CYS A:76 , GLN A:92 , ALA B:79
BINDING SITE FOR RESIDUE DMS A1125
05
AC5
SOFTWARE
PRO A:14 , ARG A:15 , THR A:16 , LEU B:105 , LYS B:106 , DMS B:1126
BINDING SITE FOR RESIDUE DMS B1124
06
AC6
SOFTWARE
VAL B:12 , PRO B:14 , LEU B:29 , GLN B:72
BINDING SITE FOR RESIDUE DMS A1140
07
AC7
SOFTWARE
LYS A:22 , GLY A:24 , CYS A:25 , CYS A:27 , LEU A:29 , PEG A:1131 , HOH A:2009 , HOH A:2015
BINDING SITE FOR RESIDUE DMS A1126
08
AC8
SOFTWARE
LYS B:22 , GLY B:24 , CYS B:27 , GLY B:28 , LEU B:29 , GLY B:30 , HOH B:2009
BINDING SITE FOR RESIDUE DMS B1125
09
AC9
SOFTWARE
THR A:16 , LEU B:105 , LEU B:108 , DMS B:1124
BINDING SITE FOR RESIDUE DMS B1126
10
BC1
SOFTWARE
PRO A:78 , ALA A:79 , LEU B:75 , CYS B:76 , GLN B:92
BINDING SITE FOR RESIDUE DMS B1127
11
BC2
SOFTWARE
LEU A:114 , LEU B:3 , GLU B:4 , ARG B:64 , TRP B:67
BINDING SITE FOR RESIDUE DMS B1128
12
BC3
SOFTWARE
VAL A:74 , GLN A:92 , ASN A:96 , HOH A:2038
BINDING SITE FOR RESIDUE DMS A1141
13
BC4
SOFTWARE
TRP A:67 , GLN A:68 , CYS A:69 , HOH A:2006 , PEG B:1131
BINDING SITE FOR RESIDUE PEG A1127
14
BC5
SOFTWARE
GLY A:28 , GLY A:30 , ASP A:47 , LYS A:61 , CA A:200 , PEG A:1133 , 9JH A:1134
BINDING SITE FOR RESIDUE PEG A1128
15
BC6
SOFTWARE
LEU B:29 , LYS B:61 , ASN B:71 , GLN B:72 , ASN B:96 , HOH B:2005
BINDING SITE FOR RESIDUE PEG B1129
16
BC7
SOFTWARE
ARG A:64 , SER A:66 , GLU A:80 , GLN B:68 , PEG B:1131
BINDING SITE FOR RESIDUE PEG A1129
17
BC8
SOFTWARE
ALA A:19
BINDING SITE FOR RESIDUE PEG A1130
18
BC9
SOFTWARE
TRP B:67 , CYS B:69 , HOH B:2024
BINDING SITE FOR RESIDUE PEG B1130
19
CC1
SOFTWARE
TYR A:65 , SER A:66 , TRP A:67 , PEG A:1127 , PEG A:1129 , HOH A:2005 , GLN B:34
BINDING SITE FOR RESIDUE PEG B1131
20
CC2
SOFTWARE
LEU A:29 , GLY A:31 , HIS A:32 , GLN A:100 , GLN A:112 , DMS A:1126
BINDING SITE FOR RESIDUE PEG A1131
21
CC3
SOFTWARE
ALA A:38 , THR A:101 , GLU A:102 , GLN A:112
BINDING SITE FOR RESIDUE PEG A1132
22
CC4
SOFTWARE
LEU A:29 , LYS A:61 , GLN A:72 , SER A:73 , ASN A:96 , PEG A:1128
BINDING SITE FOR RESIDUE PEG A1133
23
CC5
SOFTWARE
GLY B:28 , GLY B:30 , ASP B:47 , THR B:51 , GLU B:54 , CA B:200
BINDING SITE FOR RESIDUE PEG B1132
24
CC6
SOFTWARE
LEU A:5 , PRO A:17 , TYR A:20 , MET A:21 , PHE A:26 , CYS A:27 , GLY A:28 , CYS A:43 , HIS A:46 , ASP A:47 , ILE A:94 , CA A:200 , PEG A:1128
BINDING SITE FOR RESIDUE 9JH A1134
25
CC7
SOFTWARE
PRO B:17 , TYR B:20 , PHE B:26 , CYS B:27 , GLY B:28 , CYS B:43 , HIS B:46 , ASP B:47 , ILE B:94 , CA B:200
BINDING SITE FOR RESIDUE 9JH B1133
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
Info
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;
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Sorry, no Info available
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
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CATH Domains
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Pfam Domains
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Sorry, no Info available
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Asymmetric Unit 1
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Miscellaneous
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Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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Note:
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View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
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In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
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Asym.Unit (52 KB)
Header - Asym.Unit
Biol.Unit 1 (24 KB)
Header - Biol.Unit 1
Biol.Unit 2 (24 KB)
Header - Biol.Unit 2
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