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4OGB
Asym. Unit
Info
Asym.Unit (239 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (61 KB)
Biol.Unit 3 (61 KB)
Biol.Unit 4 (62 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PDE4D2 WITH COMPOUND 2
Authors
:
S. C. Feil, M. W. Parker
Date
:
15 Jan 14 (Deposition) - 21 Jan 15 (Release) - 21 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.03
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-Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. L. Howard, J. L. Nankervis, S. C. Feil, D. T. Manallack, J. K. Holien, Z. Zhen, I. G. Jennings, B. M. Abbott, M. W. Parker, P. E. Thompson
The Pde Inhibition Profile Of Ly294002 And Tetrahydropyrany Analogues Reveals A Chromone Motif For The Development Of Pde Inhibitors
To Be Published
[
close entry info
]
Hetero Components
(6, 55)
Info
All Hetero Components
1a: (2R)-8-(3,4-DIMETHOXYPHENYL)-6-MET... (2SRa)
1b: (2R)-8-(3,4-DIMETHOXYPHENYL)-6-MET... (2SRb)
1c: (2R)-8-(3,4-DIMETHOXYPHENYL)-6-MET... (2SRc)
1d: (2R)-8-(3,4-DIMETHOXYPHENYL)-6-MET... (2SRd)
2a: DIMETHYL SULFOXIDE (DMSa)
2b: DIMETHYL SULFOXIDE (DMSb)
2c: DIMETHYL SULFOXIDE (DMSc)
2d: DIMETHYL SULFOXIDE (DMSd)
2e: DIMETHYL SULFOXIDE (DMSe)
2f: DIMETHYL SULFOXIDE (DMSf)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
3ae: 1,2-ETHANEDIOL (EDOae)
3af: 1,2-ETHANEDIOL (EDOaf)
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)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
5a: DI(HYDROXYETHYL)ETHER (PEGa)
5b: DI(HYDROXYETHYL)ETHER (PEGb)
5c: DI(HYDROXYETHYL)ETHER (PEGc)
5d: DI(HYDROXYETHYL)ETHER (PEGd)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
6e: ZINC ION (ZNe)
6f: ZINC ION (ZNf)
6g: ZINC ION (ZNg)
6h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
2SR
4
Ligand/Ion
(2R)-8-(3,4-DIMETHOXYPHENYL)-6-METHYL-2-(TETRAHYDRO-2H-PYRAN-4-YL)-2H-CHROMEN-4-OL
2
DMS
6
Ligand/Ion
DIMETHYL SULFOXIDE
3
EDO
32
Ligand/Ion
1,2-ETHANEDIOL
4
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5
PEG
4
Ligand/Ion
DI(HYDROXYETHYL)ETHER
6
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(55, 55)
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)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: DC7 (SOFTWARE)
35: DC8 (SOFTWARE)
36: DC9 (SOFTWARE)
37: EC1 (SOFTWARE)
38: EC2 (SOFTWARE)
39: EC3 (SOFTWARE)
40: EC4 (SOFTWARE)
41: EC5 (SOFTWARE)
42: EC6 (SOFTWARE)
43: EC7 (SOFTWARE)
44: EC8 (SOFTWARE)
45: EC9 (SOFTWARE)
46: FC1 (SOFTWARE)
47: FC2 (SOFTWARE)
48: FC3 (SOFTWARE)
49: FC4 (SOFTWARE)
50: FC5 (SOFTWARE)
51: FC6 (SOFTWARE)
52: FC7 (SOFTWARE)
53: FC8 (SOFTWARE)
54: FC9 (SOFTWARE)
55: GC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:160 , MET A:273 , LEU A:319 , MET A:357 , SER A:368 , GLN A:369 , PHE A:372 , ILE A:376
BINDING SITE FOR RESIDUE 2SR A 501
02
AC2
SOFTWARE
GLU A:218 , LYS C:239
BINDING SITE FOR RESIDUE EDO A 502
03
AC3
SOFTWARE
LEU A:132 , LYS A:136 , HOH A:628 , ASP D:394
BINDING SITE FOR RESIDUE EDO A 503
04
AC4
SOFTWARE
GLU A:150 , ASP A:151 , TYR A:153 , HOH A:640 , ARG C:346
BINDING SITE FOR RESIDUE PEG A 504
05
AC5
SOFTWARE
LYS A:255 , GLN A:256 , GLU D:182 , DMS D:504
BINDING SITE FOR RESIDUE EDO A 505
06
AC6
SOFTWARE
PHE A:238 , PHE A:249 , ARG A:257 , HOH A:609 , HOH A:631
BINDING SITE FOR RESIDUE EDO A 506
07
AC7
SOFTWARE
ASN A:278
BINDING SITE FOR RESIDUE EDO A 507
08
AC8
SOFTWARE
LYS A:239 , GLN A:242 , GLU A:243 , HOH A:608 , ASN C:216 , GLN D:242
BINDING SITE FOR RESIDUE EDO A 508
09
AC9
SOFTWARE
HIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , HOH A:668 , HOH A:707
BINDING SITE FOR RESIDUE ZN A 509
10
BC1
SOFTWARE
ASP A:201 , HOH A:606 , HOH A:614 , HOH A:616 , HOH A:668 , HOH A:708
BINDING SITE FOR RESIDUE ZN A 510
11
BC2
SOFTWARE
PRO A:138 , ASP A:140 , THR A:141 , HOH A:686
BINDING SITE FOR RESIDUE DMS A 511
12
BC3
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH A:633 , HOH B:616
BINDING SITE FOR RESIDUE EDO A 512
13
BC4
SOFTWARE
HIS A:105 , VAL A:106 , PHE A:107 , ARG A:108 , GLN A:327 , GLN A:331
BINDING SITE FOR RESIDUE DMS A 513
14
BC5
SOFTWARE
HIS A:152 , GLU A:243 , SER C:217 , ARG C:350
BINDING SITE FOR RESIDUE EDO A 514
15
BC6
SOFTWARE
HIS B:160 , MET B:273 , LEU B:319 , MET B:357 , SER B:368 , GLN B:369 , PHE B:372 , DMS B:510 , HOH B:613
BINDING SITE FOR RESIDUE 2SR B 501
16
BC7
SOFTWARE
HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , HOH B:617 , HOH B:690
BINDING SITE FOR RESIDUE ZN B 502
17
BC8
SOFTWARE
ASP B:201 , HOH B:603 , HOH B:606 , HOH B:609 , HOH B:617 , HOH B:689
BINDING SITE FOR RESIDUE ZN B 503
18
BC9
SOFTWARE
SER B:208 , PHE B:340 , PRO B:356 , CYS B:358 , HOH B:692
BINDING SITE FOR RESIDUE EDO B 504
19
CC1
SOFTWARE
PHE B:107 , GLN B:331 , ASP B:334 , ARG B:335
BINDING SITE FOR RESIDUE EDO B 505
20
CC2
SOFTWARE
GLN A:258 , ASN B:214 , EDO B:507 , HOH B:625 , SER D:294 , SER D:295
BINDING SITE FOR RESIDUE EDO B 506
21
CC3
SOFTWARE
PHE B:211 , ASN B:214 , GLU B:347 , MET B:352 , GLU B:353 , SER B:355 , EDO B:506 , HOH B:625
BINDING SITE FOR RESIDUE EDO B 507
22
CC4
SOFTWARE
ALA B:183
BINDING SITE FOR RESIDUE EDO B 508
23
CC5
SOFTWARE
LYS B:101 , TRP B:102 , GLY B:103 , LEU B:104 , VAL B:106 , ASP B:167 , GLN B:170 , LYS B:324
BINDING SITE FOR RESIDUE EDO B 509
24
CC6
SOFTWARE
TYR B:159 , ASN B:321 , PRO B:322 , THR B:333 , PHE B:372 , 2SR B:501
BINDING SITE FOR RESIDUE DMS B 510
25
CC7
SOFTWARE
ASP B:140
BINDING SITE FOR RESIDUE EDO B 511
26
CC8
SOFTWARE
GLU B:349 , ARG B:350 , ASP D:140 , ILE D:143 , THR D:144
BINDING SITE FOR RESIDUE DMS B 512
27
CC9
SOFTWARE
THR C:148 , HIS C:152 , GLU C:243
BINDING SITE FOR RESIDUE EDO C 501
28
DC1
SOFTWARE
HIS C:160 , MET C:273 , LEU C:319 , MET C:357 , GLN C:369 , PHE C:372
BINDING SITE FOR RESIDUE 2SR C 502
29
DC2
SOFTWARE
ASN C:115 , ALA C:155 , ASN C:161 , ASN C:162 , ILE C:163 , ARG C:335
BINDING SITE FOR RESIDUE EDO C 503
30
DC3
SOFTWARE
HIS B:389 , PRO B:390 , THR C:134 , PHE C:135 , ASN C:251 , GLN C:256
BINDING SITE FOR RESIDUE EDO C 504
31
DC4
SOFTWARE
PRO B:179 , LEU C:188 , LYS C:255
BINDING SITE FOR RESIDUE EDO C 505
32
DC5
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 506
33
DC6
SOFTWARE
LYS C:262 , ASP C:266 , ASN D:224 , ASP D:225
BINDING SITE FOR RESIDUE EDO C 507
34
DC7
SOFTWARE
ASP C:266 , LEU C:269 , LYS C:275 , GLN C:311
BINDING SITE FOR RESIDUE EDO C 508
35
DC8
SOFTWARE
ASN C:115 , GLU C:150 , ASP C:151 , TYR C:153 , ASN C:162
BINDING SITE FOR RESIDUE EDO C 509
36
DC9
SOFTWARE
HIS C:164 , HIS C:200 , ASP C:201 , ASP C:318 , HOH C:601 , HOH C:666
BINDING SITE FOR RESIDUE ZN C 510
37
EC1
SOFTWARE
ASP C:201 , HOH C:602 , HOH C:613 , HOH C:664 , HOH C:665 , HOH C:666
BINDING SITE FOR RESIDUE ZN C 511
38
EC2
SOFTWARE
LEU C:219 , MET C:222 , TYR C:223
BINDING SITE FOR RESIDUE EDO C 512
39
EC3
SOFTWARE
LEU C:175 , THR C:178 , TRP C:384 , ASP C:391 , ALA C:392
BINDING SITE FOR RESIDUE EDO C 513
40
EC4
SOFTWARE
PHE B:211 , THR B:215 , ARG B:350 , THR D:148 , HIS D:152 , GLU D:243 , HOH D:691
BINDING SITE FOR RESIDUE EDO D 501
41
EC5
SOFTWARE
HIS D:160 , MET D:273 , LEU D:319 , PHE D:340 , MET D:357 , SER D:368 , GLN D:369 , PHE D:372 , ILE D:376
BINDING SITE FOR RESIDUE 2SR D 502
42
EC6
SOFTWARE
THR D:178 , TRP D:384 , VAL D:388 , ASP D:391 , PEG D:515 , PEG D:516 , HOH D:671
BINDING SITE FOR RESIDUE EDO D 503
43
EC7
SOFTWARE
EDO A:505 , SER D:177 , GLU D:182
BINDING SITE FOR RESIDUE DMS D 504
44
EC8
SOFTWARE
VAL D:120 , HIS D:123
BINDING SITE FOR RESIDUE EDO D 505
45
EC9
SOFTWARE
ASP D:266 , GLN D:311 , PEG D:507
BINDING SITE FOR RESIDUE EDO D 506
46
FC1
SOFTWARE
ASP C:225 , HOH C:628 , LYS D:262 , ASP D:266 , EDO D:506 , HOH D:670
BINDING SITE FOR RESIDUE PEG D 507
47
FC2
SOFTWARE
GLU D:150 , ASP D:151 , TYR D:153 , ASN D:162 , EDO D:510
BINDING SITE FOR RESIDUE DMS D 508
48
FC3
SOFTWARE
ASP D:266 , LYS D:275 , GLN D:311
BINDING SITE FOR RESIDUE EDO D 509
49
FC4
SOFTWARE
ASN D:115 , ALA D:155 , ASN D:161 , ASN D:162 , ILE D:163 , DMS D:508
BINDING SITE FOR RESIDUE EDO D 510
50
FC5
SOFTWARE
GLU D:128 , HIS D:173 , SER D:177
BINDING SITE FOR RESIDUE EDO D 511
51
FC6
SOFTWARE
HIS D:164 , HIS D:200 , ASP D:201 , ASP D:318 , HOH D:711 , HOH D:712
BINDING SITE FOR RESIDUE ZN D 512
52
FC7
SOFTWARE
ASP D:201 , HOH D:606 , HOH D:623 , HOH D:662 , HOH D:711 , HOH D:713
BINDING SITE FOR RESIDUE ZN D 513
53
FC8
SOFTWARE
THR A:134 , ASN A:251 , GLN A:256 , PRO D:179 , ASP D:391 , HOH D:717
BINDING SITE FOR RESIDUE EDO D 514
54
FC9
SOFTWARE
THR A:134 , HOH A:661 , ASP D:391 , EDO D:503 , PEG D:516 , HOH D:717
BINDING SITE FOR RESIDUE PEG D 515
55
GC1
SOFTWARE
LYS D:101 , TRP D:102 , VAL D:174 , ASP D:394 , ILE D:395 , EDO D:503 , PEG D:515 , HOH D:615
BINDING SITE FOR RESIDUE PEG D 516
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
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;
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Sorry, no Info available
[
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Exons
(0, 0)
Info
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Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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CATH Domains
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Pfam Domains
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