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4UY1
Asym. Unit
Info
Asym.Unit (51 KB)
Biol.Unit 1 (24 KB)
Biol.Unit 2 (24 KB)
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(1)
Title
:
NOVEL PYRAZOLE SERIES OF GROUP X SECRETORY PHOSPHOLIPASE A2 (SPLA2-X) INHIBITORS
Authors
:
J. Sandmark, L. Oster, K. Hallberg, C. Bodin, H. Chen
Date
:
28 Aug 14 (Deposition) - 15 Oct 14 (Release) - 17 Dec 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Hydrolase, Fragment Based Lead Generation, Virtual Screening, Drug Discovery
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Chen, L. Knerr, T. Akerud, K. Hallberg, C. Bodin, L. Oster, M. Rohman K. Osterlund, H. G. Beisel, T. Olsson, J. Brengdhal, J. Sandmark
Discovery Of A Novel Pyrazole Series Of Group X Secreted Phospholipase A2 Inhibitor (Spla2X) Via Fragment Based Virtual Screening
Bioorg. Med. Chem. Lett. V. 24 5251 2014
[
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Hetero Components
(5, 20)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
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)
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)
5a: 5-(2,5-DIMETHYL-3-THIENYL)-1H-PYRA... (TJMa)
5b: 5-(2,5-DIMETHYL-3-THIENYL)-1H-PYRA... (TJMb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
3
Ligand/Ion
PENTAETHYLENE GLYCOL
2
CA
2
Ligand/Ion
CALCIUM ION
3
DMS
7
Ligand/Ion
DIMETHYL SULFOXIDE
4
PEG
6
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
TJM
2
Ligand/Ion
5-(2,5-DIMETHYL-3-THIENYL)-1H-PYRAZOLE-3-CARBOXAMIDE
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Sites
(20, 20)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE A:26 , GLY A:28 , GLY A:30 , ASP A:47 , 1PE A:1125 , TJM A:1130
BINDING SITE FOR RESIDUE CA A 200
02
AC2
SOFTWARE
PHE B:26 , GLY B:28 , GLY B:30 , ASP B:47 , TJM B:1129 , HOH B:2008
BINDING SITE FOR RESIDUE CA B 200
03
AC3
SOFTWARE
ARG A:15 , TYR A:103 , LEU B:105 , LEU B:108
BINDING SITE FOR RESIDUE 1PE A1124
04
AC4
SOFTWARE
ILE A:2 , GLY A:28 , LEU A:29 , GLY A:30 , ASP A:47 , LYS A:61 , GLN A:72 , CA A:200 , TJM A:1130 , HOH A:2027 , HOH A:2067
BINDING SITE FOR RESIDUE 1PE A1125
05
AC5
SOFTWARE
LEU B:29 , HIS B:46 , ASP B:47 , TYR B:50 , LYS B:61 , GLN B:72 , SER B:73 , ASN B:96 , TJM B:1129 , HOH B:2008 , HOH B:2045
BINDING SITE FOR RESIDUE 1PE B1125
06
AC6
SOFTWARE
PRO A:78 , ALA A:79 , LEU B:75 , CYS B:76 , GLN B:92
BINDING SITE FOR RESIDUE DMS B1126
07
AC7
SOFTWARE
CYS A:76 , GLN A:92 , PRO B:78 , ALA B:79
BINDING SITE FOR RESIDUE DMS A1126
08
AC8
SOFTWARE
LYS B:22 , GLY B:24 , CYS B:27 , GLY B:28 , LEU B:29
BINDING SITE FOR RESIDUE DMS B1127
09
AC9
SOFTWARE
GLY A:24 , CYS A:25 , PHE A:26 , CYS A:27 , GLY A:28 , LEU A:29 , GLY A:30
BINDING SITE FOR RESIDUE DMS A1127
10
BC1
SOFTWARE
GLU A:54 , SER A:59 , PRO A:60 , LYS A:61 , LEU A:75 , HOH A:2055
BINDING SITE FOR RESIDUE DMS A1128
11
BC2
SOFTWARE
ASP A:47 , TYR A:50 , THR A:51 , GLU A:54
BINDING SITE FOR RESIDUE DMS A1129
12
BC3
SOFTWARE
ARG A:36 , TYR A:107 , TYR A:110 , GLY B:7
BINDING SITE FOR RESIDUE DMS B1128
13
BC4
SOFTWARE
LEU A:5 , PRO A:17 , TYR A:20 , PHE A:26 , GLY A:28 , CYS A:43 , HIS A:46 , ASP A:47 , CA A:200 , 1PE A:1125 , HOH A:2068
BINDING SITE FOR RESIDUE TJM A1130
14
BC5
SOFTWARE
ILE B:2 , LEU B:5 , ALA B:6 , PRO B:17 , TYR B:20 , MET B:21 , PHE B:26 , GLY B:28 , CYS B:43 , HIS B:46 , ASP B:47 , ILE B:94 , CA B:200 , 1PE B:1125
BINDING SITE FOR RESIDUE TJM B1129
15
BC6
SOFTWARE
TRP A:67 , GLN A:68 , CYS A:69 , PEG A:1132 , HOH A:2005
BINDING SITE FOR RESIDUE PEG A1131
16
BC7
SOFTWARE
ALA A:6 , GLY A:7 , GLY A:10 , CYS A:11 , PEG A:1131 , ARG B:36 , TYR B:107 , TYR B:110
BINDING SITE FOR RESIDUE PEG A1132
17
BC8
SOFTWARE
SER B:59 , PRO B:60 , LYS B:61 , VAL B:74 , GLN B:92 , ASN B:96
BINDING SITE FOR RESIDUE PEG B1130
18
BC9
SOFTWARE
LEU A:114 , LEU B:3 , GLU B:4 , ARG B:64 , TYR B:65 , TRP B:67 , HOH B:2024
BINDING SITE FOR RESIDUE PEG B1131
19
CC1
SOFTWARE
ARG A:64 , SER A:66 , PRO A:78 , GLU A:80 , GLN B:68 , LEU B:75
BINDING SITE FOR RESIDUE PEG A1133
20
CC2
SOFTWARE
ALA B:38 , TRP B:41 , CYS B:97 , GLN B:112
BINDING SITE FOR RESIDUE PEG B1132
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
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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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Asymmetric Unit 1
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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:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
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 (51 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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