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3WD9
Asym. Unit
Info
Asym.Unit (127 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (63 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PHOSPHODIESTERASE 4B IN COMPLEX WITH COMPOUND 10F
Authors
:
M. Takahashi, H. Hanzawa
Date
:
11 Jun 13 (Deposition) - 23 Oct 13 (Release) - 23 Oct 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Phosphodiesterase, Copd, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Goto, A. Shiina, T. Yoshino, K. Mizukami, K. Hirahara, O. Suzuki, Y. Sogawa, T. Takahashi, T. Mikkaichi, N. Nakao, M. Takahashi, M. Hasegawa, S. Sasaki
Synthesis And Biological Evaluation Of 5-Carbamoyl-2-Phenylpyrimidine Derivatives As Novel And Potent Pde4 Inhibitors
Bioorg. Med. Chem. V. 21 7025 2013
[
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 4-[(4-{2-[(2,2-DIMETHYLPROPYL)AMIN... (QPCa)
2b: 4-[(4-{2-[(2,2-DIMETHYLPROPYL)AMIN... (QPCb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
QPC
2
Ligand/Ion
4-[(4-{2-[(2,2-DIMETHYLPROPYL)AMINO]-2-OXOETHYL}PHENYL)AMINO]-2-PHENYLPYRIMIDINE-5-CARBOXAMIDE
3
ZN
2
Ligand/Ion
ZINC ION
[
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]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:233 , SER A:282 , ASN A:395 , PHE A:414 , SER A:442 , GLN A:443 , PHE A:446 , LEU A:502 , MET A:503 , PHE A:506 , GLU A:509 , HOH A:1055 , HOH A:1093 , HOH A:1111 , HOH A:1121 , HOH A:1153
BINDING SITE FOR RESIDUE QPC A 901
2
AC2
SOFTWARE
HIS A:238 , HIS A:274 , ASP A:275 , ASP A:392 , HOH A:1004 , HOH A:1007
BINDING SITE FOR RESIDUE ZN A 902
3
AC3
SOFTWARE
ASP A:275 , HOH A:1001 , HOH A:1002 , HOH A:1003 , HOH A:1004 , HOH A:1006
BINDING SITE FOR RESIDUE CA A 903
4
AC4
SOFTWARE
TYR B:233 , GLY B:280 , VAL B:281 , SER B:282 , ASN B:395 , ILE B:410 , GLU B:413 , PHE B:414 , GLN B:417 , SER B:442 , GLN B:443 , PHE B:446 , LEU B:502 , HOH B:1040 , HOH B:1053 , HOH B:1077 , HOH B:1176
BINDING SITE FOR RESIDUE QPC B 901
5
AC5
SOFTWARE
HIS B:238 , HIS B:274 , ASP B:275 , ASP B:392 , HOH B:1004 , HOH B:1006
BINDING SITE FOR RESIDUE ZN B 902
6
AC6
SOFTWARE
ASP B:275 , HOH B:1001 , HOH B:1002 , HOH B:1003 , HOH B:1005 , HOH B:1006
BINDING SITE FOR RESIDUE CA B 903
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:274-285,B:274-285)
;
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.
PDE4B_HUMAN
446-457
2
A:274-285
B:274-285
[
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]
Exons
(8, 16)
Info
All Exons
Exon 1.21 (A:154-168 | B:154-168)
Exon 1.22e (A:169-201 | B:169-201)
Exon 1.23b (A:202-256 | B:202-256)
Exon 1.24 (A:257-290 | B:257-290)
Exon 1.25b (A:290-341 | B:290-341)
Exon 1.26a (A:342-382 | B:342-382)
Exon 1.27 (A:383-443 | B:383-443)
Exon 1.28c (A:444-511 (gaps) | B:444-511 (gaps...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.19b/1.21
2: Boundary 1.21/1.22e
3: Boundary 1.22e/1.23b
4: Boundary 1.23b/1.24
5: Boundary 1.24/1.25b
6: Boundary 1.25b/1.26a
7: Boundary 1.26a/1.27
8: Boundary 1.27/1.28c
9: Boundary 1.28c/-
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
1.2
ENST00000341517
2
ENSE00001777645
chr1:
66258864-66258931
68
PDE4B_HUMAN
-
0
0
-
-
1.3a
ENST00000341517
3a
ENSE00001454221
chr1:
66378928-66379039
112
PDE4B_HUMAN
1-14
14
0
-
-
1.4
ENST00000341517
4
ENSE00001314677
chr1:
66384280-66384518
239
PDE4B_HUMAN
15-94
80
0
-
-
1.10c
ENST00000341517
10c
ENSE00001295605
chr1:
66713143-66713337
195
PDE4B_HUMAN
94-159
66
0
-
-
1.12
ENST00000341517
12
ENSE00001648425
chr1:
66723330-66723366
37
PDE4B_HUMAN
159-171
13
0
-
-
1.13
ENST00000341517
13
ENSE00001301262
chr1:
66723476-66723546
71
PDE4B_HUMAN
172-195
24
0
-
-
1.14a
ENST00000341517
14a
ENSE00001328762
chr1:
66731721-66731770
50
PDE4B_HUMAN
195-212
18
0
-
-
1.17e
ENST00000341517
17e
ENSE00001765348
chr1:
66798191-66798303
113
PDE4B_HUMAN
212-249
38
0
-
-
1.19b
ENST00000341517
19b
ENSE00001321190
chr1:
66821210-66821303
94
PDE4B_HUMAN
250-281
32
0
-
-
1.21
ENST00000341517
21
ENSE00001308616
chr1:
66827298-66827476
179
PDE4B_HUMAN
281-340
60
2
A:154-168
B:154-168
15
15
1.22e
ENST00000341517
22e
ENSE00001292510
chr1:
66828851-66828949
99
PDE4B_HUMAN
341-373
33
2
A:169-201
B:169-201
33
33
1.23b
ENST00000341517
23b
ENSE00001311355
chr1:
66829090-66829254
165
PDE4B_HUMAN
374-428
55
2
A:202-256
B:202-256
55
55
1.24
ENST00000341517
24
ENSE00001294554
chr1:
66831350-66831449
100
PDE4B_HUMAN
429-462
34
2
A:257-290
B:257-290
34
34
1.25b
ENST00000341517
25b
ENSE00001326709
chr1:
66833379-66833533
155
PDE4B_HUMAN
462-513
52
2
A:290-341
B:290-341
52
52
1.26a
ENST00000341517
26a
ENSE00001304431
chr1:
66833626-66833748
123
PDE4B_HUMAN
514-554
41
2
A:342-382
B:342-382
41
41
1.27
ENST00000341517
27
ENSE00001597852
chr1:
66834470-66834652
183
PDE4B_HUMAN
555-615
61
2
A:383-443
B:383-443
61
61
1.28c
ENST00000341517
28c
ENSE00002180148
chr1:
66837996-66839187
1192
PDE4B_HUMAN
616-736
121
2
A:444-511 (gaps)
B:444-511 (gaps)
68
68
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3wd9a_ (A:)
1b: SCOP_d3wd9b_ (B:)
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Classes
(
)
(
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Folds
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(
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(
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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 4b2b
(28)
Human (Homo sapiens) [TaxId: 9606]
(28)
1a
d3wd9a_
A:
1b
d3wd9b_
B:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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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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Nucleic
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Asymmetric Unit 1
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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Asym.Unit (127 KB)
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Biol.Unit 1 (63 KB)
Header - Biol.Unit 1
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