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3SL5
Asym. Unit
Info
Asym.Unit (233 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (60 KB)
Biol.Unit 3 (60 KB)
Biol.Unit 4 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PDE4D2 COMPLEXED WITH COMPOUND 10D
Authors
:
S. F. Feil
Date
:
24 Jun 11 (Deposition) - 26 Oct 11 (Release) - 14 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.65
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Catalytic Mechanism, Camp Hydrolysis, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. L. Nankervis, S. C. Feil, N. C. Hancock, Z. Zheng, H. L. Ng, C. J. Morton, J. K. Holien, P. W. Ho, M. M. Frazzetto, I. G. Jennings, D. T. Manallack, T. J. Martin, P. E. Thompson, M. W. Parker
Thiophene Inhibitors Of Pde4: Crystal Structures Show A Second Binding Mode At The Catalytic Domain Of Pde4D2.
Bioorg. Med. Chem. Lett. V. 21 7089 2011
[
close entry info
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Hetero Components
(5, 31)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4a: DIETHYL 2-[(THIOPHEN-2-YLACETYL)AM... (J25a)
4b: DIETHYL 2-[(THIOPHEN-2-YLACETYL)AM... (J25b)
4c: DIETHYL 2-[(THIOPHEN-2-YLACETYL)AM... (J25c)
4d: DIETHYL 2-[(THIOPHEN-2-YLACETYL)AM... (J25d)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
5g: ZINC ION (ZNg)
5h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
1
Ligand/Ion
DIMETHYL SULFOXIDE
2
EDO
17
Ligand/Ion
1,2-ETHANEDIOL
3
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
J25
4
Ligand/Ion
DIETHYL 2-[(THIOPHEN-2-YLACETYL)AMINO]-4,7-DIHYDROTHIENO[2,3-C]PYRIDINE-3,6(5H)-DICARBOXYLATE
5
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
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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:585
BINDING SITE FOR RESIDUE ZN A 438
02
AC2
SOFTWARE
ASP A:201 , HOH A:528 , HOH A:529 , HOH A:597
BINDING SITE FOR RESIDUE ZN A 439
03
AC3
SOFTWARE
TYR A:159 , MET A:273 , ASN A:321 , PRO A:322 , TYR A:329 , PHE A:340 , MET A:357 , SER A:368 , GLN A:369 , PHE A:372 , ILE A:376
BINDING SITE FOR RESIDUE J25 A 1
04
AC4
SOFTWARE
LYS A:262 , ASP A:266 , HOH B:567
BINDING SITE FOR RESIDUE EDO A 2
05
AC5
SOFTWARE
ASP A:140 , THR A:141
BINDING SITE FOR RESIDUE DMS A 3
06
AC6
SOFTWARE
THR A:186 , LEU A:188 , GLU A:189 , EDO D:4
BINDING SITE FOR RESIDUE EDO A 4
07
AC7
SOFTWARE
HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , ZN B:439 , HOH B:564
BINDING SITE FOR RESIDUE ZN B 438
08
AC8
SOFTWARE
ASP B:201 , ZN B:438 , HOH B:527 , HOH B:566 , HOH B:580 , HOH B:587
BINDING SITE FOR RESIDUE ZN B 439
09
AC9
SOFTWARE
TYR B:159 , MET B:273 , LEU B:319 , ASN B:321 , PRO B:322 , TYR B:329 , THR B:333 , MET B:337 , PHE B:340 , MET B:357 , GLN B:369 , PHE B:372 , HOH B:591
BINDING SITE FOR RESIDUE J25 B 1
10
BC1
SOFTWARE
GLU B:218 , LEU C:221
BINDING SITE FOR RESIDUE EDO B 2
11
BC2
SOFTWARE
HIS B:160 , HIS B:204 , GLY B:206 , VAL B:207 , GLU B:339 , PHE B:340 , GLN B:343
BINDING SITE FOR RESIDUE EDO B 3
12
BC3
SOFTWARE
HIS C:105 , VAL C:106 , PHE C:107 , ARG C:108 , GLU C:111 , GLN C:327 , LEU C:328 , GLN C:331
BINDING SITE FOR RESIDUE EPE C 5
13
BC4
SOFTWARE
HIS C:164 , HIS C:200 , ASP C:201 , ASP C:318 , ZN C:439 , HOH C:523 , HOH C:556
BINDING SITE FOR RESIDUE ZN C 438
14
BC5
SOFTWARE
ASP C:201 , ZN C:438 , HOH C:520 , HOH C:523 , HOH C:564 , HOH C:581
BINDING SITE FOR RESIDUE ZN C 439
15
BC6
SOFTWARE
TYR C:159 , MET C:273 , ASN C:321 , TYR C:329 , TRP C:332 , THR C:333 , ILE C:336 , PHE C:340 , SER C:368 , GLN C:369 , PHE C:372 , ILE C:376 , HOH C:522
BINDING SITE FOR RESIDUE J25 C 1
16
BC7
SOFTWARE
HIS B:389 , PRO B:390 , THR C:134 , PHE C:135 , LYS C:136 , ASN C:251 , GLN C:256
BINDING SITE FOR RESIDUE EDO C 2
17
BC8
SOFTWARE
GLU B:182 , LEU C:188 , LYS C:255 , SER C:259
BINDING SITE FOR RESIDUE EDO C 3
18
BC9
SOFTWARE
GLU C:97 , GLU C:128
BINDING SITE FOR RESIDUE EDO C 4
19
CC1
SOFTWARE
ASP C:98 , LYS C:101 , TRP C:102 , GLY C:103 , HIS C:105
BINDING SITE FOR RESIDUE EDO C 6
20
CC2
SOFTWARE
ASP C:266 , LYS C:275 , GLN C:311
BINDING SITE FOR RESIDUE EDO C 7
21
CC3
SOFTWARE
THR B:215 , SER B:217 , HIS D:152 , GLU D:243 , HOH D:527
BINDING SITE FOR RESIDUE EDO D 2
22
CC4
SOFTWARE
GLN C:242 , ASN D:216 , LEU D:221
BINDING SITE FOR RESIDUE EDO D 5
23
CC5
SOFTWARE
HIS D:164 , HIS D:200 , ASP D:201 , ASP D:318 , ZN D:439 , HOH D:606
BINDING SITE FOR RESIDUE ZN D 438
24
CC6
SOFTWARE
ASP D:201 , ZN D:438 , HOH D:532 , HOH D:542 , HOH D:625
BINDING SITE FOR RESIDUE ZN D 439
25
CC7
SOFTWARE
TYR D:159 , MET D:273 , LEU D:319 , ASN D:321 , PRO D:322 , TYR D:329 , MET D:357 , SER D:368 , GLN D:369 , PHE D:372 , ILE D:376 , HOH D:607
BINDING SITE FOR RESIDUE J25 D 1
26
CC8
SOFTWARE
LEU D:181 , ALA D:183 , VAL D:184 , PHE D:185 , ILE D:190 , HOH D:596 , HOH D:619
BINDING SITE FOR RESIDUE EDO D 3
27
CC9
SOFTWARE
EDO A:4 , LEU A:188 , LYS A:255 , GLN A:256 , GLU D:182
BINDING SITE FOR RESIDUE EDO D 4
28
DC1
SOFTWARE
THR D:178 , ILE D:395 , HOH D:605
BINDING SITE FOR RESIDUE EDO D 6
29
DC2
SOFTWARE
THR A:134 , ASN A:251 , GLN A:256 , PRO D:179 , ASP D:391
BINDING SITE FOR RESIDUE EDO D 8
30
DC3
SOFTWARE
ASN D:115 , ARG D:116 , GLU D:150 , ASP D:151 , TYR D:153
BINDING SITE FOR RESIDUE EDO D 7
31
DC4
SOFTWARE
ASN D:115 , HOH D:583
BINDING SITE FOR RESIDUE EDO D 9
[
close Site info
]
SAPs(SNPs)/Variants
(4, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_068245 (T285P, chain A/B/C/D, )
2: VAR_069453 (E288A, chain A/B/C/D, )
3: VAR_069454 (G371D, chain A/B/C/D, )
4: VAR_069455 (I376T, chain A/B/C/D, )
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/C/D
T
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B/C/D
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B/C/D
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B/C/D
I
376
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:200-211,B:200-211,C:200-211,D:20...)
;
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
4
A:200-211
B:200-211
C:200-211
D:200-211
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.34 (A:83-94 | B:88-94 | C:86-94 | D:88...)
Exon 1.35 (A:95-127 | B:95-127 | C:95-127 | D...)
Exon 1.36 (A:128-182 | B:128-182 | C:128-182 ...)
Exon 1.37 (A:183-216 | B:183-216 | C:183-216 ...)
Exon 1.38 (A:216-267 | B:216-267 | C:216-267 ...)
Exon 1.39 (A:268-308 | B:268-308 | C:268-308 ...)
Exon 1.40 (A:309-369 | B:309-369 | C:309-369 ...)
Exon 1.41j (A:370-410 | B:370-412 | C:370-410 ...)
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
4
A:83-94
B:88-94
C:86-94
D:88-94
12
7
9
7
1.35
ENST00000340635
35
ENSE00001001090
chr5:
58286729-58286631
99
PDE4D_HUMAN
397-429
33
4
A:95-127
B:95-127
C:95-127
D:95-127
33
33
33
33
1.36
ENST00000340635
36
ENSE00001001087
chr5:
58285746-58285582
165
PDE4D_HUMAN
430-484
55
4
A:128-182
B:128-182
C:128-182
D:128-182
55
55
55
55
1.37
ENST00000340635
37
ENSE00001001091
chr5:
58284419-58284320
100
PDE4D_HUMAN
485-518
34
4
A:183-216
B:183-216
C:183-216
D:183-216
34
34
34
34
1.38
ENST00000340635
38
ENSE00001175221
chr5:
58273172-58273018
155
PDE4D_HUMAN
518-569
52
4
A:216-267
B:216-267
C:216-267
D:216-267
52
52
52
52
1.39
ENST00000340635
39
ENSE00001001088
chr5:
58272299-58272177
123
PDE4D_HUMAN
570-610
41
4
A:268-308
B:268-308
C:268-308
D:268-308
41
41
41
41
1.40
ENST00000340635
40
ENSE00001698537
chr5:
58271666-58271484
183
PDE4D_HUMAN
611-671
61
4
A:309-369
B:309-369
C:309-369
D:309-369
61
61
61
61
1.41j
ENST00000340635
41j
ENSE00001989721
chr5:
58270907-58264865
6043
PDE4D_HUMAN
672-809
138
4
A:370-410
B:370-412
C:370-410
D:370-411
41
43
41
42
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3sl5a_ (A:)
1b: SCOP_d3sl5b_ (B:)
1c: SCOP_d3sl5c_ (C:)
1d: SCOP_d3sl5d_ (D:)
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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
d3sl5a_
A:
1b
d3sl5b_
B:
1c
d3sl5c_
C:
1d
d3sl5d_
D:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Pfam Domains
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all PFAM domains
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Asym.Unit (233 KB)
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