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3SL4
Biol. Unit 4
Info
Asym.Unit (244 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (63 KB)
Biol.Unit 3 (63 KB)
Biol.Unit 4 (64 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PDE4D2 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
:
1.90
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
(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, 24)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
1b: DIMETHYL SULFOXIDE (DMSb)
1c: DIMETHYL SULFOXIDE (DMSc)
1d: DIMETHYL SULFOXIDE (DMSd)
1e: DIMETHYL SULFOXIDE (DMSe)
1f: DIMETHYL SULFOXIDE (DMSf)
1g: DIMETHYL SULFOXIDE (DMSg)
1h: DIMETHYL SULFOXIDE (DMSh)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2ae: 1,2-ETHANEDIOL (EDOae)
2af: 1,2-ETHANEDIOL (EDOaf)
2ag: 1,2-ETHANEDIOL (EDOag)
2ah: 1,2-ETHANEDIOL (EDOah)
2ai: 1,2-ETHANEDIOL (EDOai)
2aj: 1,2-ETHANEDIOL (EDOaj)
2ak: 1,2-ETHANEDIOL (EDOak)
2al: 1,2-ETHANEDIOL (EDOal)
2am: 1,2-ETHANEDIOL (EDOam)
2an: 1,2-ETHANEDIOL (EDOan)
2ao: 1,2-ETHANEDIOL (EDOao)
2ap: 1,2-ETHANEDIOL (EDOap)
2aq: 1,2-ETHANEDIOL (EDOaq)
2ar: 1,2-ETHANEDIOL (EDOar)
2as: 1,2-ETHANEDIOL (EDOas)
2at: 1,2-ETHANEDIOL (EDOat)
2au: 1,2-ETHANEDIOL (EDOau)
2av: 1,2-ETHANEDIOL (EDOav)
2aw: 1,2-ETHANEDIOL (EDOaw)
2ax: 1,2-ETHANEDIOL (EDOax)
2ay: 1,2-ETHANEDIOL (EDOay)
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)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
3b: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEb)
4a: ETHENYL 6-(ETHENYLCARBAMOYL)-2-[(P... (JN4a)
4b: ETHENYL 6-(ETHENYLCARBAMOYL)-2-[(P... (JN4b)
4c: ETHENYL 6-(ETHENYLCARBAMOYL)-2-[(P... (JN4c)
4d: ETHENYL 6-(ETHENYLCARBAMOYL)-2-[(P... (JN4d)
5a: DI(HYDROXYETHYL)ETHER (PEGa)
5b: DI(HYDROXYETHYL)ETHER (PEGb)
5c: DI(HYDROXYETHYL)ETHER (PEGc)
5d: DI(HYDROXYETHYL)ETHER (PEGd)
5e: DI(HYDROXYETHYL)ETHER (PEGe)
6a: PHOSPHATE ION (PO4a)
6b: PHOSPHATE ION (PO4b)
6c: PHOSPHATE ION (PO4c)
6d: PHOSPHATE ION (PO4d)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
7c: ZINC ION (ZNc)
7d: ZINC ION (ZNd)
7e: ZINC ION (ZNe)
7f: ZINC ION (ZNf)
7g: ZINC ION (ZNg)
7h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
4
Ligand/Ion
DIMETHYL SULFOXIDE
2
EDO
14
Ligand/Ion
1,2-ETHANEDIOL
3
EPE
-1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
JN4
1
Ligand/Ion
ETHENYL 6-(ETHENYLCARBAMOYL)-2-[(PHENYLACETYL)AMINO]-4,5,6,7-TETRAHYDROTHIENO[2,3-C]PYRIDINE-3-CARBOXYLATE
5
PEG
4
Ligand/Ion
DI(HYDROXYETHYL)ETHER
6
PO4
1
Ligand/Ion
PHOSPHATE ION
7
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(30, 30)
Info
All Sites
01: BC2 (SOFTWARE)
02: CC1 (SOFTWARE)
03: DC3 (SOFTWARE)
04: FC5 (SOFTWARE)
05: GC3 (SOFTWARE)
06: GC4 (SOFTWARE)
07: GC5 (SOFTWARE)
08: GC6 (SOFTWARE)
09: GC7 (SOFTWARE)
10: GC8 (SOFTWARE)
11: GC9 (SOFTWARE)
12: HC1 (SOFTWARE)
13: HC2 (SOFTWARE)
14: HC3 (SOFTWARE)
15: HC4 (SOFTWARE)
16: HC5 (SOFTWARE)
17: HC6 (SOFTWARE)
18: HC7 (SOFTWARE)
19: HC8 (SOFTWARE)
20: HC9 (SOFTWARE)
21: IC1 (SOFTWARE)
22: IC2 (SOFTWARE)
23: IC3 (SOFTWARE)
24: IC4 (SOFTWARE)
25: IC5 (SOFTWARE)
26: IC6 (SOFTWARE)
27: IC7 (SOFTWARE)
28: IC8 (SOFTWARE)
29: IC9 (SOFTWARE)
30: JC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
BC2
SOFTWARE
EDO A:18 , LEU A:188 , LYS A:255 , GLN A:256 , SER A:259 , DMS D:8 , GLU D:182
BINDING SITE FOR RESIDUE EDO A 13
02
CC1
SOFTWARE
LYS A:239 , GLN A:242 , HOH A:547 , ASN C:216 , LYS D:239 , GLN D:242
BINDING SITE FOR RESIDUE EDO A 21
03
DC3
SOFTWARE
GLN A:258 , EDO A:441 , ASN B:214 , HOH B:515 , SER D:294 , SER D:295
BINDING SITE FOR RESIDUE EDO B 9
04
FC5
SOFTWARE
LYS C:262 , ASP C:266 , ASN D:224 , ASP D:225
BINDING SITE FOR RESIDUE EDO C 11
05
GC3
SOFTWARE
THR B:215 , ARG B:350 , HOH B:528 , THR D:148 , HIS D:152 , GLU D:243 , HOH D:495
BINDING SITE FOR RESIDUE EDO D 5
06
GC4
SOFTWARE
EDO D:7 , ASN D:100 , LYS D:101 , TRP D:102 , VAL D:174 , HOH D:447 , HOH D:534
BINDING SITE FOR RESIDUE PEG D 12
07
GC5
SOFTWARE
PO4 D:24 , HIS D:164 , HIS D:200 , ASP D:201 , ASP D:318 , HOH D:482
BINDING SITE FOR RESIDUE ZN D 1
08
GC6
SOFTWARE
PO4 D:24 , HOH D:76 , ASP D:201 , HOH D:482 , HOH D:546 , HOH D:557
BINDING SITE FOR RESIDUE ZN D 2
09
GC7
SOFTWARE
THR A:134 , ASN A:251 , GLN A:256 , HOH A:460 , PRO D:179 , ASP D:391
BINDING SITE FOR RESIDUE EDO D 4
10
GC8
SOFTWARE
LEU D:181 , ALA D:183 , VAL D:184 , PHE D:185 , HOH D:449
BINDING SITE FOR RESIDUE EDO D 440
11
GC9
SOFTWARE
ASN D:115
BINDING SITE FOR RESIDUE EDO D 6
12
HC1
SOFTWARE
PEG D:12 , LEU D:175 , THR D:178 , ASP D:391 , HOH D:473
BINDING SITE FOR RESIDUE EDO D 7
13
HC2
SOFTWARE
EDO A:13 , HOH A:477 , SER D:177 , THR D:178 , PRO D:179 , GLU D:182
BINDING SITE FOR RESIDUE DMS D 8
14
HC3
SOFTWARE
GLU B:349 , ARG B:350 , ASP D:140 , THR D:144
BINDING SITE FOR RESIDUE DMS D 9
15
HC4
SOFTWARE
HIS D:123
BINDING SITE FOR RESIDUE EDO D 10
16
HC5
SOFTWARE
EDO D:14 , ASP D:266 , GLN D:311
BINDING SITE FOR RESIDUE EDO D 11
17
HC6
SOFTWARE
ASP C:225 , HOH C:464 , GLN D:258 , LYS D:262 , ASP D:266
BINDING SITE FOR RESIDUE PEG D 441
18
HC7
SOFTWARE
EDO D:17 , ASN D:115 , GLU D:150 , ASP D:151 , TYR D:153 , ASN D:162
BINDING SITE FOR RESIDUE DMS D 13
19
HC8
SOFTWARE
EDO D:11 , ASP D:266 , LYS D:275 , GLN D:311
BINDING SITE FOR RESIDUE EDO D 14
20
HC9
SOFTWARE
MET D:286 , THR D:289 , LYS D:291 , LEU D:299
BINDING SITE FOR RESIDUE EDO D 15
21
IC1
SOFTWARE
PRO D:325 , LEU D:326 , ASP D:401 , ASN D:402
BINDING SITE FOR RESIDUE PEG D 16
22
IC2
SOFTWARE
DMS D:13 , ASN D:115 , ALA D:155 , ASN D:161 , ASN D:162
BINDING SITE FOR RESIDUE EDO D 17
23
IC3
SOFTWARE
ASN D:100 , GLU D:128 , HIS D:173 , SER D:177 , HOH D:472
BINDING SITE FOR RESIDUE EDO D 18
24
IC4
SOFTWARE
ASP D:156 , VAL D:157 , ALA D:158 , PRO D:205 , GLU D:339 , ARG D:346 , HOH D:476
BINDING SITE FOR RESIDUE PEG D 19
25
IC5
SOFTWARE
ASN C:231 , LEU C:234 , PHE C:238 , ARG C:261 , LEU D:221 , ASN D:224 , HOH D:488
BINDING SITE FOR RESIDUE EDO D 20
26
IC6
SOFTWARE
ASN C:231 , EDO D:22 , MET D:222 , TYR D:223 , ASN D:224 , SER D:226 , ASN D:231 , HOH D:452 , HOH D:468
BINDING SITE FOR RESIDUE EDO D 21
27
IC7
SOFTWARE
EDO D:21 , SER D:226 , ASN D:231 , HOH D:468
BINDING SITE FOR RESIDUE EDO D 22
28
IC8
SOFTWARE
HIS D:105 , VAL D:106 , PHE D:107 , ARG D:108 , GLN D:327 , LEU D:328 , GLN D:331
BINDING SITE FOR RESIDUE DMS D 23
29
IC9
SOFTWARE
ZN D:1 , ZN D:2 , HIS D:160 , HIS D:164 , ASP D:201 , ASP D:318 , JN4 D:442 , HOH D:482 , HOH D:483 , HOH D:518
BINDING SITE FOR RESIDUE PO4 D 24
30
JC1
SOFTWARE
PO4 D:24 , TYR D:159 , MET D:273 , LEU D:319 , ASN D:321 , PRO D:322 , TYR D:329 , THR D:333 , ILE D:336 , MET D:337 , MET D:357 , SER D:368 , GLN D:369 , PHE D:372 , HOH D:483 , HOH D:554 , HOH D:559
BINDING SITE FOR RESIDUE JN4 D 442
[
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]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_068245 (T285P, chain D, )
2: VAR_069453 (E288A, chain D, )
3: VAR_069454 (G371D, chain D, )
4: VAR_069455 (I376T, chain 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)
---
D
T
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
D
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
D
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
D
I
376
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (D: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
1
-
-
-
D:200-211
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3sl4a_ (A:)
1b: SCOP_d3sl4b_ (B:)
1c: SCOP_d3sl4c_ (C:)
1d: SCOP_d3sl4d_ (D:)
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Protein Domains
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(
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Organisms
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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
d3sl4a_
A:
1b
d3sl4b_
B:
1c
d3sl4c_
C:
1d
d3sl4d_
D:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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Chain D
Asymmetric Unit 1
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Asym.Unit (244 KB)
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