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1Y2D
Asym. Unit
Info
Asym.Unit (130 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (63 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH 1-(4-METHOXY-PHENYL)-3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER
Authors
:
G. L. Card, L. Blasdel, B. P. England, C. Zhang, Y. Suzuki, S. Gillette, D P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. Milburn, S. -H. Kim, J. Schle K. Y. J. Zhang
Date
:
22 Nov 04 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Phosphodiesterase, Pde, Pde4D, Pyrazole, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. L. Card, L. Blasdel, B. P. England, C. Zhang, Y. Suzuki, S. Gillette, D. Fong, P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. Milburn, S. -H. Kim, J. Schlessinger, K. Y. J. Zhang
A Family Of Phosphodiesterase Inhibitors Discovered By Cocrystallography And Scaffold-Based Drug Design
Nat. Biotechnol. V. 23 201 2005
[
close entry info
]
Hetero Components
(5, 31)
Info
All Hetero Components
1a: 1-(4-METHOXYPHENYL)-3,5-DIMETHYL-1... (4DEa)
1b: 1-(4-METHOXYPHENYL)-3,5-DIMETHYL-1... (4DEb)
2a: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHY... (B3Pa)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
4DE
2
Ligand/Ion
1-(4-METHOXYPHENYL)-3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER
2
B3P
1
Ligand/Ion
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3
EDO
24
Ligand/Ion
1,2-ETHANEDIOL
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(31, 31)
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)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , HOH A:1007 , HOH A:1008
BINDING SITE FOR RESIDUE ZN A 1001
02
AC2
SOFTWARE
ASP A:201 , HOH A:1003 , HOH A:1004 , HOH A:1005 , HOH A:1006 , HOH A:1007
BINDING SITE FOR RESIDUE MG A 1002
03
AC3
SOFTWARE
HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , MG B:1002 , HOH B:2007 , HOH B:2008
BINDING SITE FOR RESIDUE ZN B 1001
04
AC4
SOFTWARE
ASP B:201 , ZN B:1001 , HOH B:2003 , HOH B:2004 , HOH B:2005 , HOH B:2006 , HOH B:2007
BINDING SITE FOR RESIDUE MG B 1002
05
AC5
SOFTWARE
MET A:273 , THR A:333 , MET A:357 , GLN A:369 , PHE A:372
BINDING SITE FOR RESIDUE 4DE A 601
06
AC6
SOFTWARE
ASN B:321 , THR B:333 , ILE B:336 , MET B:357 , GLN B:369 , PHE B:372 , HOH B:2266
BINDING SITE FOR RESIDUE 4DE B 602
07
AC7
SOFTWARE
PRO A:411 , GLU B:366 , TYR B:406 , HOH B:2068
BINDING SITE FOR RESIDUE EDO B 701
08
AC8
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH A:1020
BINDING SITE FOR RESIDUE EDO A 702
09
AC9
SOFTWARE
ASN A:209 , GLN A:210 , HOH A:1012 , HOH A:1025 , HOH A:1028 , HOH A:1049
BINDING SITE FOR RESIDUE EDO A 703
10
BC1
SOFTWARE
SER B:208 , PRO B:356 , HOH B:2183
BINDING SITE FOR RESIDUE EDO B 704
11
BC2
SOFTWARE
PRO A:179 , GLY A:296 , HIS A:389 , ASP A:391 , HOH A:1228
BINDING SITE FOR RESIDUE EDO A 705
12
BC3
SOFTWARE
ASN A:115 , ALA A:155 , ASN A:161 , ASN A:162 , ARG A:335 , HOH A:1219
BINDING SITE FOR RESIDUE EDO A 706
13
BC4
SOFTWARE
LEU A:175 , THR A:178 , TRP A:384 , VAL A:388 , ASP A:391 , ALA A:392 , HOH A:1147
BINDING SITE FOR RESIDUE EDO A 707
14
BC5
SOFTWARE
PHE B:238 , ARG B:257 , ARG B:261 , HOH B:2081 , HOH B:2098
BINDING SITE FOR RESIDUE EDO B 708
15
BC6
SOFTWARE
PHE A:238 , ARG A:257 , HOH A:1047 , HOH A:1100
BINDING SITE FOR RESIDUE EDO A 709
16
BC7
SOFTWARE
SER A:208 , PHE A:340 , PRO A:356 , HOH A:1064
BINDING SITE FOR RESIDUE EDO A 710
17
BC8
SOFTWARE
GLY A:371 , PHE A:372
BINDING SITE FOR RESIDUE EDO A 711
18
BC9
SOFTWARE
LYS B:262 , ILE B:265 , ASP B:266 , HOH B:2039
BINDING SITE FOR RESIDUE EDO B 712
19
CC1
SOFTWARE
GLU B:150 , ASP B:151 , TYR B:153 , ASN B:162 , EDO B:718 , HOH B:2011 , HOH B:2074 , HOH B:2180
BINDING SITE FOR RESIDUE EDO B 713
20
CC2
SOFTWARE
ASP B:401 , ASN B:402 , HOH B:2012 , HOH B:2108 , HOH B:2181
BINDING SITE FOR RESIDUE EDO B 714
21
CC3
SOFTWARE
ASP B:156 , VAL B:157 , ALA B:158 , GLU B:339 , ARG B:342 , HOH B:2025 , HOH B:2060
BINDING SITE FOR RESIDUE EDO B 715
22
CC4
SOFTWARE
ILE A:213 , ASN A:216 , SER A:217 , ALA A:220 , LEU A:221 , ASP A:225 , ARG B:261
BINDING SITE FOR RESIDUE EDO A 716
23
CC5
SOFTWARE
HIS A:154 , ASP A:203 , PRO A:205
BINDING SITE FOR RESIDUE EDO A 717
24
CC6
SOFTWARE
ASN B:115 , ALA B:155 , ASN B:162 , EDO B:713 , HOH B:2074
BINDING SITE FOR RESIDUE EDO B 718
25
CC7
SOFTWARE
GLU A:366 , HOH A:1081
BINDING SITE FOR RESIDUE EDO A 719
26
CC8
SOFTWARE
ALA A:183 , VAL A:184 , ASN B:115 , ARG B:116 , HOH B:2180
BINDING SITE FOR RESIDUE EDO A 720
27
CC9
SOFTWARE
HOH A:1079 , GLN B:327 , HOH B:2118 , HOH B:2215
BINDING SITE FOR RESIDUE EDO B 721
28
DC1
SOFTWARE
ARG A:330 , HOH B:2012 , HOH B:2091 , HOH B:2236
BINDING SITE FOR RESIDUE EDO B 722
29
DC2
SOFTWARE
THR B:178 , TRP B:384 , ASP B:391 , EDO B:724 , HOH B:2190
BINDING SITE FOR RESIDUE EDO B 723
30
DC3
SOFTWARE
ASP B:394 , EDO B:723 , HOH B:2126 , HOH B:2142 , HOH B:2256
BINDING SITE FOR RESIDUE EDO B 724
31
DC4
SOFTWARE
ASP A:397 , ASP A:401 , HOH A:1132 , LYS B:94 , GLU B:95 , GLU B:97 , ASP B:98 , HIS B:105
BINDING SITE FOR RESIDUE B3P B 801
[
close Site info
]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_068245 (T285P, chain A/B, )
2: VAR_069453 (E288A, chain A/B, )
3: VAR_069454 (G371D, chain A/B, )
4: VAR_069455 (I376T, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_068245
T
587
P
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B
T
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B
I
376
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:200-211,B:200-211)
;
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.
PDE4D_HUMAN
502-513
2
A:200-211
B:200-211
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.34 (A:86-94 | B:86-94)
Exon 1.35 (A:95-127 | B:95-127)
Exon 1.36 (A:128-182 | B:128-182)
Exon 1.37 (A:183-216 | B:183-216)
Exon 1.38 (A:216-267 | B:216-267)
Exon 1.39 (A:268-308 | B:268-308)
Exon 1.40 (A:309-369 | B:309-369)
Exon 1.41j (A:370-411 | B:370-411)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.33b/1.34
2: Boundary 1.34/1.35
3: Boundary 1.35/1.36
4: Boundary 1.36/1.37
5: Boundary 1.37/1.38
6: Boundary 1.38/1.39
7: Boundary 1.39/1.40
8: Boundary 1.40/1.41j
9: Boundary 1.41j/-
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
1.13a
ENST00000340635
13a
ENSE00001559328
chr5:
59189625-59188995
631
PDE4D_HUMAN
1-152
152
0
-
-
1.21b
ENST00000340635
21b
ENSE00001136096
chr5:
58511794-58511603
192
PDE4D_HUMAN
152-216
65
0
-
-
1.22
ENST00000340635
22
ENSE00001682119
chr5:
58489362-58489326
37
PDE4D_HUMAN
216-228
13
0
-
-
1.23
ENST00000340635
23
ENSE00001754547
chr5:
58481088-58481015
74
PDE4D_HUMAN
229-253
25
0
-
-
1.24
ENST00000340635
24
ENSE00001719283
chr5:
58476470-58476421
50
PDE4D_HUMAN
253-270
18
0
-
-
1.31d
ENST00000340635
31d
ENSE00001750566
chr5:
58334798-58334686
113
PDE4D_HUMAN
270-307
38
0
-
-
1.33b
ENST00000340635
33b
ENSE00000914184
chr5:
58289292-58289199
94
PDE4D_HUMAN
308-339
32
0
-
-
1.34
ENST00000340635
34
ENSE00001136103
chr5:
58287831-58287659
173
PDE4D_HUMAN
339-396
58
2
A:86-94
B:86-94
9
9
1.35
ENST00000340635
35
ENSE00001001090
chr5:
58286729-58286631
99
PDE4D_HUMAN
397-429
33
2
A:95-127
B:95-127
33
33
1.36
ENST00000340635
36
ENSE00001001087
chr5:
58285746-58285582
165
PDE4D_HUMAN
430-484
55
2
A:128-182
B:128-182
55
55
1.37
ENST00000340635
37
ENSE00001001091
chr5:
58284419-58284320
100
PDE4D_HUMAN
485-518
34
2
A:183-216
B:183-216
34
34
1.38
ENST00000340635
38
ENSE00001175221
chr5:
58273172-58273018
155
PDE4D_HUMAN
518-569
52
2
A:216-267
B:216-267
52
52
1.39
ENST00000340635
39
ENSE00001001088
chr5:
58272299-58272177
123
PDE4D_HUMAN
570-610
41
2
A:268-308
B:268-308
41
41
1.40
ENST00000340635
40
ENSE00001698537
chr5:
58271666-58271484
183
PDE4D_HUMAN
611-671
61
2
A:309-369
B:309-369
61
61
1.41j
ENST00000340635
41j
ENSE00001989721
chr5:
58270907-58264865
6043
PDE4D_HUMAN
672-809
138
2
A:370-411
B:370-411
42
42
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1y2da_ (A:)
1b: SCOP_d1y2db_ (B:)
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Class
:
All alpha proteins
(14657)
Fold
:
HD-domain/PDEase-like
(204)
Superfamily
:
HD-domain/PDEase-like
(204)
Family
:
PDEase
(118)
Protein domain
:
Catalytic domain of cyclic nucleotide phosphodiesterase pde4d
(33)
Human (Homo sapiens) [TaxId: 9606]
(33)
1a
d1y2da_
A:
1b
d1y2db_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1y2dA00 (A:86-411)
1b: CATH_1y2dB00 (B:86-411)
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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
1y2dA00
A:86-411
1b
1y2dB00
B:86-411
[
close CATH info
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDEase_I_1y2dB01 (B:159-403)
1b: PFAM_PDEase_I_1y2dB02 (B:159-403)
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(
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Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1y2dB01
B:159-403
1b
PDEase_I-1y2dB02
B:159-403
[
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