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2CHM
Asym. Unit
Info
Asym.Unit (71 KB)
Biol.Unit 1 (65 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF N2 SUBSTITUTED PYRAZOLO PYRIMIDINONES-A FLIPPED BINDING MODE IN PDE5
Authors
:
C. M. N. Allerton, C. G. Barber, K. C. Beaumont, D. G. Brown, S. M. Cole, D. Ellis, C. A. L. Lane, G. N. Maw, N. M. Mount, D. J. Rawson, C. M. Robinson, S. D. A. Street, N. W. Summerhill
Date
:
15 Mar 06 (Deposition) - 08 Jun 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Phosphodiesterase 5, Inhibitor, Chimera, Allosteric Enzyme, Alternative Splicing, Cgmp, Cgmp-Binding, Hydrolase, Magnesium, Metal-Binding, Nucleotide-Binding, Phosphorylation, Zinc, Camp
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. M. N. Allerton, C. G. Barber, K. C. Beaumont, D. G. Brown, S. M. Cole, D. Ellis, C. A. L. Lane, G. N. Maw, N. M. Mount, D. J. Rawson, C. M. Robinson, S. D. A. Street, N. W. Summerhill
A Novel Series Of Potent And Selective Pde5 Inhibitors With Potential For High And Dose- Independent Oral Bioavailability
J. Med. Chem. V. 49 3581 2006
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Hetero Components
(4, 4)
Info
All Hetero Components
1a: 5-[2-(BUT-3-EN-1-YLOXY)-5-(1-HYDRO... (3P4a)
2a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
3a: MAGNESIUM ION (MGa)
4a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
3P4
1
Ligand/Ion
5-[2-(BUT-3-EN-1-YLOXY)-5-(1-HYDROXYVINYL)PYRIDIN-3-YL]-3-ETHYL-2-(1-ETHYLAZETIDIN-3-YL)-1,2,6,7A-TETRAHYDRO-7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
2
MES
1
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:617 , HIS A:653 , ASP A:654 , ASP A:764 , HOH A:2508 , HOH A:2509
BINDING SITE FOR RESIDUE ZN A1859
2
AC2
SOFTWARE
ASP A:654 , HOH A:2118 , HOH A:2182 , HOH A:2222 , HOH A:2223 , HOH A:2508
BINDING SITE FOR RESIDUE MG A1860
3
AC3
SOFTWARE
ALA A:545 , LEU A:725 , LEU A:765 , ALA A:767 , ILE A:768 , GLN A:775 , ALA A:779 , VAL A:782 , ALA A:783 , LEU A:804 , MET A:816 , GLN A:817 , PHE A:820 , HOH A:2510 , HOH A:2511 , HOH A:2512
BINDING SITE FOR RESIDUE 3P4 A1861
4
AC4
SOFTWARE
ARG A:607 , LYS A:608 , ASN A:609 , ASN A:742 , GLN A:743 , PHE A:744 , ASN A:745 , HOH A:2154 , HOH A:2513 , HOH A:2514 , HOH A:2515
BINDING SITE FOR RESIDUE MES A1862
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:653-662)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PDEASE_I
PS00126
3'5'-cyclic nucleotide phosphodiesterases signature.
PDE5A_HUMAN
653-664
1
A:653-662
[
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Exons
(11, 11)
Info
All Exons
Exon 1.15b (A:537-544)
Exon 1.18 (A:545-593)
Exon 1.19b (A:594-635)
Exon 1.20c (A:636-667)
Exon 1.22 (A:667-696)
Exon 1.23b (A:697-730)
Exon 1.24b (A:730-756)
Exon 1.25 (A:756-777)
Exon 1.26a (A:778-802)
Exon 1.27a (A:803-830)
Exon 1.28c (A:831-858)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.13/1.15b
02: Boundary 1.15b/1.18
03: Boundary 1.18/1.19b
04: Boundary 1.19b/1.20c
05: Boundary 1.20c/1.22
06: Boundary 1.22/1.23b
07: Boundary 1.23b/1.24b
08: Boundary 1.24b/1.25
09: Boundary 1.25/1.26a
10: Boundary 1.26a/1.27a
11: Boundary 1.27a/1.28c
12: Boundary 1.28c/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000354960
1a
ENSE00001851914
chr4:
120550146-120549675
472
PDE5A_HUMAN
1-51
51
0
-
-
1.4
ENST00000354960
4
ENSE00001637089
chr4:
120528452-120527864
589
PDE5A_HUMAN
51-247
197
0
-
-
1.5b
ENST00000354960
5b
ENSE00000935544
chr4:
120517767-120517678
90
PDE5A_HUMAN
248-277
30
0
-
-
1.6
ENST00000354960
6
ENSE00000970323
chr4:
120488299-120488228
72
PDE5A_HUMAN
278-301
24
0
-
-
1.7
ENST00000354960
7
ENSE00000970324
chr4:
120486565-120486476
90
PDE5A_HUMAN
302-331
30
0
-
-
1.8b
ENST00000354960
8b
ENSE00000970325
chr4:
120484125-120483988
138
PDE5A_HUMAN
332-377
46
0
-
-
1.9
ENST00000354960
9
ENSE00000970326
chr4:
120481518-120481451
68
PDE5A_HUMAN
378-400
23
0
-
-
1.10
ENST00000354960
10
ENSE00000970327
chr4:
120474901-120474793
109
PDE5A_HUMAN
400-436
37
0
-
-
1.11a
ENST00000354960
11a
ENSE00000970328
chr4:
120473792-120473705
88
PDE5A_HUMAN
437-466
30
0
-
-
1.13
ENST00000354960
13
ENSE00000935541
chr4:
120463789-120463614
176
PDE5A_HUMAN
466-524
59
0
-
-
1.15b
ENST00000354960
15b
ENSE00000935545
chr4:
120460174-120460115
60
PDE5A_HUMAN
525-544
20
1
A:537-544
8
1.18
ENST00000354960
18
ENSE00001016848
chr4:
120446850-120446704
147
PDE5A_HUMAN
545-593
49
1
A:545-593
49
1.19b
ENST00000354960
19b
ENSE00001016844
chr4:
120442215-120442090
126
PDE5A_HUMAN
594-635
42
1
A:594-635
42
1.20c
ENST00000354960
20c
ENSE00001016846
chr4:
120440294-120440200
95
PDE5A_HUMAN
636-667
32
1
A:636-667
32
1.22
ENST00000354960
22
ENSE00001016843
chr4:
120432289-120432202
88
PDE5A_HUMAN
667-696
30
1
A:667-696
31
1.23b
ENST00000354960
23b
ENSE00001016840
chr4:
120428859-120428759
101
PDE5A_HUMAN
697-730
34
1
A:697-730
34
1.24b
ENST00000354960
24b
ENSE00001016847
chr4:
120427087-120427010
78
PDE5A_HUMAN
730-756
27
1
A:730-756
27
1.25
ENST00000354960
25
ENSE00001016842
chr4:
120425754-120425691
64
PDE5A_HUMAN
756-777
22
1
A:756-777
22
1.26a
ENST00000354960
26a
ENSE00001016841
chr4:
120423810-120423736
75
PDE5A_HUMAN
778-802
25
1
A:778-802
25
1.27a
ENST00000354960
27a
ENSE00001016845
chr4:
120422408-120422325
84
PDE5A_HUMAN
803-830
28
1
A:803-830
28
1.28c
ENST00000354960
28c
ENSE00001890486
chr4:
120419893-120415550
4344
PDE5A_HUMAN
831-875
45
1
A:831-858
28
[
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d2chma1 (A:537-858)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
HD-domain/PDEase-like
(204)
Superfamily
:
HD-domain/PDEase-like
(204)
Family
:
PDEase
(118)
Protein domain
:
cGMP-specific 3',5'-cyclic phosphodiesterase pde5a1-Ibmx
(17)
Human (Homo sapiens) [TaxId: 9606]
(17)
1a
d2chma1
A:537-858
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_2chmA00 (A:537-858)
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Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
(66)
Homologous Superfamily
:
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
(66)
Human (Homo sapiens)
(64)
1a
2chmA00
A:537-858
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Pfam Domains
(0, 0)
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all PFAM domains
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Chain A
Asymmetric Unit 1
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