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3SL8
Biol. Unit 4
Info
Asym.Unit (233 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (59 KB)
Biol.Unit 3 (60 KB)
Biol.Unit 4 (61 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PDE4D2 WITH COMPOUND 10O
Authors
:
S. F. Feil
Date
:
24 Jun 11 (Deposition) - 26 Oct 11 (Release) - 14 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
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
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Hetero Components
(4, 15)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
1b: DIMETHYL SULFOXIDE (DMSb)
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)
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: 3-CYCLOPENTYL 6-ETHENYL 2-[(THIOPH... (JN7a)
3b: 3-CYCLOPENTYL 6-ETHENYL 2-[(THIOPH... (JN7b)
3c: 3-CYCLOPENTYL 6-ETHENYL 2-[(THIOPH... (JN7c)
3d: 3-CYCLOPENTYL 6-ETHENYL 2-[(THIOPH... (JN7d)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
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
DMS
1
Ligand/Ion
DIMETHYL SULFOXIDE
2
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
3
JN7
1
Ligand/Ion
3-CYCLOPENTYL 6-ETHENYL 2-[(THIOPHEN-2-YLACETYL)AMINO]-4,7-DIHYDROTHIENO[2,3-C]PYRIDINE-3,6(5H)-DICARBOXYLATE
4
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PO4
-1
Ligand/Ion
PHOSPHATE ION
6
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(21, 21)
Info
All Sites
01: AC5 (SOFTWARE)
02: AC8 (SOFTWARE)
03: CC3 (SOFTWARE)
04: CC8 (SOFTWARE)
05: DC5 (SOFTWARE)
06: DC6 (SOFTWARE)
07: DC7 (SOFTWARE)
08: DC8 (SOFTWARE)
09: DC9 (SOFTWARE)
10: EC1 (SOFTWARE)
11: EC2 (SOFTWARE)
12: EC3 (SOFTWARE)
13: EC4 (SOFTWARE)
14: EC5 (SOFTWARE)
15: EC6 (SOFTWARE)
16: EC7 (SOFTWARE)
17: EC8 (SOFTWARE)
18: EC9 (SOFTWARE)
19: FC1 (SOFTWARE)
20: FC2 (SOFTWARE)
21: FC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC5
SOFTWARE
HOH A:70 , THR A:134 , PHE A:135 , ASN A:251 , GLN A:256 , ASP D:391
BINDING SITE FOR RESIDUE EDO A 6
02
AC8
SOFTWARE
GLN A:256 , GLU D:182
BINDING SITE FOR RESIDUE EDO A 9
03
CC3
SOFTWARE
ASN B:214 , MET B:352 , EDO D:7 , GLU D:244
BINDING SITE FOR RESIDUE EDO B 6
04
CC8
SOFTWARE
LYS C:262 , ASP C:266 , ASP D:225
BINDING SITE FOR RESIDUE EDO C 3
05
DC5
SOFTWARE
ASP D:266 , TYR D:303 , GLN D:311
BINDING SITE FOR RESIDUE EDO D 10
06
DC6
SOFTWARE
EDO B:6 , THR B:215 , ARG B:350 , THR D:148 , GLU D:243 , GLU D:244 , CYS D:246
BINDING SITE FOR RESIDUE EDO D 7
07
DC7
SOFTWARE
HIS D:123 , ILE D:143
BINDING SITE FOR RESIDUE EDO D 2
08
DC8
SOFTWARE
THR D:186 , LEU D:188 , SER D:259
BINDING SITE FOR RESIDUE EDO D 3
09
DC9
SOFTWARE
LEU D:175 , THR D:178 , EDO D:441
BINDING SITE FOR RESIDUE EDO D 4
10
EC1
SOFTWARE
ASP C:225 , LYS D:262 , ASP D:266
BINDING SITE FOR RESIDUE PEG D 5
11
EC2
SOFTWARE
ASP D:201 , HOH D:448 , HOH D:469 , HOH D:473
BINDING SITE FOR RESIDUE ZN D 6
12
EC3
SOFTWARE
HIS D:164 , HIS D:200 , ASP D:201 , ASP D:318 , HOH D:489
BINDING SITE FOR RESIDUE ZN D 440
13
EC4
SOFTWARE
LEU D:181 , ALA D:183 , VAL D:184 , PHE D:185 , HOH D:490
BINDING SITE FOR RESIDUE EDO D 8
14
EC5
SOFTWARE
ASP B:156 , ASP D:151 , TYR D:153 , HIS D:154 , ALA D:155 , HOH D:460
BINDING SITE FOR RESIDUE EDO D 9
15
EC6
SOFTWARE
EDO D:4 , ASN D:100 , LYS D:101 , TRP D:102 , HOH D:453
BINDING SITE FOR RESIDUE EDO D 441
16
EC7
SOFTWARE
ALA A:183 , ASN D:100 , GLU D:128
BINDING SITE FOR RESIDUE EDO D 11
17
EC8
SOFTWARE
LYS D:284 , THR D:383 , ASP D:386
BINDING SITE FOR RESIDUE EDO D 12
18
EC9
SOFTWARE
THR D:141 , ASN D:245 , CYS D:246 , ASP D:247 , GLN D:250 , HOH D:476
BINDING SITE FOR RESIDUE EDO D 13
19
FC1
SOFTWARE
ASN D:115 , ALA D:155 , ASN D:161 , ASN D:162
BINDING SITE FOR RESIDUE DMS D 14
20
FC2
SOFTWARE
HOH D:67 , MET D:277 , LEU D:280 , TYR D:375
BINDING SITE FOR RESIDUE EDO D 15
21
FC3
SOFTWARE
HOH D:22 , TYR D:159 , MET D:273 , LEU D:319 , ASN D:321 , THR D:333 , ILE D:336 , PHE D:340 , SER D:368 , GLN D:369 , PHE D:372 , ILE D:376
BINDING SITE FOR RESIDUE JN7 D 1
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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_d3sl8a_ (A:)
1b: SCOP_d3sl8b_ (B:)
1c: SCOP_d3sl8c_ (C:)
1d: SCOP_d3sl8d_ (D:)
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Protein Domains
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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
d3sl8a_
A:
1b
d3sl8b_
B:
1c
d3sl8c_
C:
1d
d3sl8d_
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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Sorry, no Info available
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Asymmetric Unit 1
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