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3LY2
Asym. Unit
Info
Asym.Unit (458 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (64 KB)
Biol.Unit 3 (62 KB)
Biol.Unit 4 (62 KB)
Biol.Unit 5 (61 KB)
Biol.Unit 6 (61 KB)
Biol.Unit 7 (62 KB)
Biol.Unit 8 (62 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4B IN COMPLEX WITH A COUMARIN-BASED INHIBITOR
Authors
:
A. K. Shiau, A. R. Coyle, J. H. Hsien, L. M. Staszewski
Date
:
26 Feb 10 (Deposition) - 28 Apr 10 (Release) - 05 May 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Biol. Unit 7: G (1x)
Biol. Unit 8: H (1x)
Keywords
:
Pde4B, Coumarin, Inhibitor, Hydrolase, Metal-Binding, Hydrolase- Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. P. Govek, G. Oshiro, J. V. Anzola, C. Beauregard, J. Chen, A. R. Coyle, D. A. Gamache, M. R. Hellberg, J. N. Hsien, J. M. Lerch, J. C. Liao, J. W. Malecha, L. M. Staszewski, D. J. Thomas, J. M. Yanni, S. A. Noble, A. K. Shiau
Water-Soluble Pde4 Inhibitors For The Treatment Of Dry Eye.
Bioorg. Med. Chem. Lett. V. 20 2928 2010
[
close entry info
]
Hetero Components
(4, 26)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
1e: MAGNESIUM ION (MGe)
1f: MAGNESIUM ION (MGf)
1g: MAGNESIUM ION (MGg)
1h: MAGNESIUM ION (MGh)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
3a: 8-(CYCLOPENTYLOXY)-4-[(3,5-DICHLOR... (Z72a)
3b: 8-(CYCLOPENTYLOXY)-4-[(3,5-DICHLOR... (Z72b)
3c: 8-(CYCLOPENTYLOXY)-4-[(3,5-DICHLOR... (Z72c)
3d: 8-(CYCLOPENTYLOXY)-4-[(3,5-DICHLOR... (Z72d)
3e: 8-(CYCLOPENTYLOXY)-4-[(3,5-DICHLOR... (Z72e)
3f: 8-(CYCLOPENTYLOXY)-4-[(3,5-DICHLOR... (Z72f)
3g: 8-(CYCLOPENTYLOXY)-4-[(3,5-DICHLOR... (Z72g)
3h: 8-(CYCLOPENTYLOXY)-4-[(3,5-DICHLOR... (Z72h)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
4f: ZINC ION (ZNf)
4g: ZINC ION (ZNg)
4h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
8
Ligand/Ion
MAGNESIUM ION
2
SO4
2
Ligand/Ion
SULFATE ION
3
Z72
8
Ligand/Ion
8-(CYCLOPENTYLOXY)-4-[(3,5-DICHLOROPYRIDIN-4-YL)AMINO]-7-METHOXY-2H-CHROMEN-2-ONE
4
ZN
8
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(26, 26)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:345 , MET A:347 , ASP A:392 , LEU A:393 , MET A:431 , SER A:442 , GLN A:443 , PHE A:446 , HOH A:1008 , HOH A:1009 , HOH A:1010 , HOH A:2120 , HOH A:2329 , HOH A:2330
BINDING SITE FOR RESIDUE Z72 A 1000
02
AC2
SOFTWARE
HIS A:238 , HIS A:274 , ASP A:275 , ASP A:392 , HOH A:1007 , HOH A:1008
BINDING SITE FOR RESIDUE ZN A 1001
03
AC3
SOFTWARE
ASP A:275 , HOH A:1004 , HOH A:1005 , HOH A:1006 , HOH A:1007 , HOH A:1010
BINDING SITE FOR RESIDUE MG A 1002
04
AC4
SOFTWARE
SER A:149 , SER A:212 , SER A:213 , HOH A:2079 , HOH A:2189
BINDING SITE FOR RESIDUE SO4 A 1003
05
AC5
SOFTWARE
THR B:345 , MET B:347 , ASP B:392 , LEU B:393 , ASN B:395 , ILE B:410 , PHE B:414 , MET B:431 , SER B:442 , GLN B:443 , PHE B:446 , HOH B:1009 , HOH B:1010 , HOH B:2070
BINDING SITE FOR RESIDUE Z72 B 1000
06
AC6
SOFTWARE
HIS B:238 , HIS B:274 , ASP B:275 , ASP B:392 , HOH B:1007 , HOH B:1008
BINDING SITE FOR RESIDUE ZN B 1001
07
AC7
SOFTWARE
ASP B:275 , HOH B:1004 , HOH B:1005 , HOH B:1006 , HOH B:1007 , HOH B:1010
BINDING SITE FOR RESIDUE MG B 1002
08
AC8
SOFTWARE
PRO B:146 , SER B:149 , SER B:212 , SER B:213 , HOH B:2062 , HOH B:2119 , HOH B:2327
BINDING SITE FOR RESIDUE SO4 B 1003
09
AC9
SOFTWARE
TYR C:233 , THR C:345 , MET C:347 , ASP C:392 , LEU C:393 , ILE C:410 , MET C:431 , SER C:442 , GLN C:443 , PHE C:446 , HOH C:1006 , HOH C:1009 , HOH C:1010
BINDING SITE FOR RESIDUE Z72 C 1000
10
BC1
SOFTWARE
HIS C:238 , HIS C:274 , ASP C:275 , ASP C:392 , HOH C:1007 , HOH C:1008
BINDING SITE FOR RESIDUE ZN C 1001
11
BC2
SOFTWARE
ASP C:275 , HOH C:1004 , HOH C:1005 , HOH C:1006 , HOH C:1007 , HOH C:1010
BINDING SITE FOR RESIDUE MG C 1002
12
BC3
SOFTWARE
TYR D:233 , HIS D:234 , THR D:345 , MET D:347 , ASP D:392 , LEU D:393 , ASN D:395 , ILE D:410 , MET D:411 , MET D:431 , SER D:442 , GLN D:443 , PHE D:446 , HOH D:1006 , HOH D:1009 , HOH D:1010 , HOH D:2127 , HOH D:2332
BINDING SITE FOR RESIDUE Z72 D 1000
13
BC4
SOFTWARE
HIS D:238 , HIS D:274 , ASP D:275 , ASP D:392 , HOH D:1007 , HOH D:1008
BINDING SITE FOR RESIDUE ZN D 1001
14
BC5
SOFTWARE
ASP D:275 , HOH D:1004 , HOH D:1005 , HOH D:1006 , HOH D:1007 , HOH D:1010
BINDING SITE FOR RESIDUE MG D 1002
15
BC6
SOFTWARE
TYR E:233 , THR E:345 , MET E:347 , ASP E:392 , LEU E:393 , ILE E:410 , MET E:431 , SER E:442 , GLN E:443 , PHE E:446 , HOH E:1006 , HOH E:1009 , HOH E:1010
BINDING SITE FOR RESIDUE Z72 E 1000
16
BC7
SOFTWARE
HIS E:238 , HIS E:274 , ASP E:275 , ASP E:392 , HOH E:1007 , HOH E:1008
BINDING SITE FOR RESIDUE ZN E 1001
17
BC8
SOFTWARE
ASP E:275 , HOH E:1004 , HOH E:1005 , HOH E:1006 , HOH E:1007 , HOH E:1010
BINDING SITE FOR RESIDUE MG E 1002
18
BC9
SOFTWARE
TYR F:233 , HIS F:234 , THR F:345 , MET F:347 , ASP F:392 , LEU F:393 , ASN F:395 , ILE F:410 , MET F:411 , MET F:431 , SER F:442 , GLN F:443 , PHE F:446 , HOH F:1006 , HOH F:1008 , HOH F:1009 , HOH F:1010
BINDING SITE FOR RESIDUE Z72 F 1000
19
CC1
SOFTWARE
HIS F:238 , HIS F:274 , ASP F:275 , ASP F:392 , HOH F:1007 , HOH F:1008
BINDING SITE FOR RESIDUE ZN F 1001
20
CC2
SOFTWARE
ASP F:275 , HOH F:1004 , HOH F:1005 , HOH F:1006 , HOH F:1007 , HOH F:1010
BINDING SITE FOR RESIDUE MG F 1002
21
CC3
SOFTWARE
THR G:345 , MET G:347 , ASP G:392 , LEU G:393 , THR G:407 , ILE G:410 , MET G:431 , SER G:442 , GLN G:443 , PHE G:446 , HOH G:1009 , HOH G:1010
BINDING SITE FOR RESIDUE Z72 G 1000
22
CC4
SOFTWARE
HIS G:238 , HIS G:274 , ASP G:275 , ASP G:392 , HOH G:1007 , HOH G:1008
BINDING SITE FOR RESIDUE ZN G 1001
23
CC5
SOFTWARE
ASP G:275 , HOH G:1004 , HOH G:1005 , HOH G:1006 , HOH G:1007 , HOH G:1010
BINDING SITE FOR RESIDUE MG G 1002
24
CC6
SOFTWARE
THR H:345 , MET H:347 , ASP H:392 , LEU H:393 , THR H:407 , ILE H:410 , MET H:431 , SER H:442 , GLN H:443 , PHE H:446 , HOH H:1009 , HOH H:1010 , HOH H:2335
BINDING SITE FOR RESIDUE Z72 H 1000
25
CC7
SOFTWARE
HIS H:238 , HIS H:274 , ASP H:275 , ASP H:392 , HOH H:1007 , HOH H:1008
BINDING SITE FOR RESIDUE ZN H 1001
26
CC8
SOFTWARE
ASP H:275 , HOH H:1004 , HOH H:1005 , HOH H:1006 , HOH H:1007 , HOH H:1010
BINDING SITE FOR RESIDUE MG H 1002
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:274-285,B:274-285,C:274-285,D:27...)
;
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
8
A:274-285
B:274-285
C:274-285
D:274-285
E:274-285
F:274-285
G:274-285
H:274-285
[
close PROSITE info
]
Exons
(9, 66)
Info
All Exons
Exon 1.19b (A:141-143 | B:141-143 | - | - | - ...)
Exon 1.21 (A:144-168 (gaps) | B:144-168 (gaps...)
Exon 1.22e (A:169-201 | B:169-201 | C:169-201 ...)
Exon 1.23b (A:202-256 | B:202-256 | C:202-256 ...)
Exon 1.24 (A:257-290 | B:257-290 | C:257-290 ...)
Exon 1.25b (A:290-341 | B:290-341 | C:290-341 ...)
Exon 1.26a (A:342-382 | B:342-382 | C:342-382 ...)
Exon 1.27 (A:383-443 | B:383-443 | C:383-443 ...)
Exon 1.28c (A:444-485 | B:444-485 | C:444-486 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.17e/1.19b
02: Boundary 1.19b/1.21
03: Boundary 1.21/1.22e
04: Boundary 1.22e/1.23b
05: Boundary 1.23b/1.24
06: Boundary 1.24/1.25b
07: Boundary 1.25b/1.26a
08: Boundary 1.26a/1.27
09: Boundary 1.27/1.28c
10: 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
2
A:141-143
B:141-143
-
-
-
-
-
-
3
3
-
-
-
-
-
-
1.21
ENST00000341517
21
ENSE00001308616
chr1:
66827298-66827476
179
PDE4B_HUMAN
281-340
60
8
A:144-168 (gaps)
B:144-168 (gaps)
C:155-168
D:158-168
E:157-168
F:158-168
G:155-168
H:155-168
37
37
14
11
12
11
14
14
1.22e
ENST00000341517
22e
ENSE00001292510
chr1:
66828851-66828949
99
PDE4B_HUMAN
341-373
33
8
A:169-201
B:169-201
C:169-201
D:169-201
E:169-201
F:169-201
G:169-201
H:169-201
33
33
33
33
33
33
33
33
1.23b
ENST00000341517
23b
ENSE00001311355
chr1:
66829090-66829254
165
PDE4B_HUMAN
374-428
55
8
A:202-256
B:202-256
C:202-256
D:202-256
E:202-256
F:202-256
G:202-256
H:202-256
55
55
55
55
55
55
55
55
1.24
ENST00000341517
24
ENSE00001294554
chr1:
66831350-66831449
100
PDE4B_HUMAN
429-462
34
8
A:257-290
B:257-290
C:257-290
D:257-290
E:257-290
F:257-290
G:257-290
H:257-290
34
34
34
34
34
34
34
34
1.25b
ENST00000341517
25b
ENSE00001326709
chr1:
66833379-66833533
155
PDE4B_HUMAN
462-513
52
8
A:290-341
B:290-341
C:290-341
D:290-341
E:290-341
F:290-341
G:290-341
H:290-341
52
52
52
52
52
52
52
52
1.26a
ENST00000341517
26a
ENSE00001304431
chr1:
66833626-66833748
123
PDE4B_HUMAN
514-554
41
8
A:342-382
B:342-382
C:342-382
D:342-382
E:342-382
F:342-382
G:342-382
H:342-382
41
41
41
41
41
41
41
41
1.27
ENST00000341517
27
ENSE00001597852
chr1:
66834470-66834652
183
PDE4B_HUMAN
555-615
61
8
A:383-443
B:383-443
C:383-443
D:383-443
E:383-443
F:383-443
G:383-443
H:383-443
61
61
61
61
61
61
61
61
1.28c
ENST00000341517
28c
ENSE00002180148
chr1:
66837996-66839187
1192
PDE4B_HUMAN
616-736
121
8
A:444-485
B:444-485
C:444-486
D:444-485
E:444-485
F:444-486
G:444-486
H:444-486
42
42
43
42
42
43
43
43
[
close EXON info
]
SCOP Domains
(1, 8)
Info
All SCOP Domains
1a: SCOP_d3ly2a_ (A:)
1b: SCOP_d3ly2b_ (B:)
1c: SCOP_d3ly2c_ (C:)
1d: SCOP_d3ly2d_ (D:)
1e: SCOP_d3ly2e_ (E:)
1f: SCOP_d3ly2f_ (F:)
1g: SCOP_d3ly2g_ (G:)
1h: SCOP_d3ly2h_ (H:)
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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 4b2b
(28)
Human (Homo sapiens) [TaxId: 9606]
(28)
1a
d3ly2a_
A:
1b
d3ly2b_
B:
1c
d3ly2c_
C:
1d
d3ly2d_
D:
1e
d3ly2e_
E:
1f
d3ly2f_
F:
1g
d3ly2g_
G:
1h
d3ly2h_
H:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
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[
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Pfam Domains
(1, 8)
Info
all PFAM domains
1a: PFAM_PDEase_I_3ly2H01 (H:233-477)
1b: PFAM_PDEase_I_3ly2H02 (H:233-477)
1c: PFAM_PDEase_I_3ly2H03 (H:233-477)
1d: PFAM_PDEase_I_3ly2H04 (H:233-477)
1e: PFAM_PDEase_I_3ly2H05 (H:233-477)
1f: PFAM_PDEase_I_3ly2H06 (H:233-477)
1g: PFAM_PDEase_I_3ly2H07 (H:233-477)
1h: PFAM_PDEase_I_3ly2H08 (H:233-477)
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(
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Organisms
(
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(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-3ly2H01
H:233-477
1b
PDEase_I-3ly2H02
H:233-477
1c
PDEase_I-3ly2H03
H:233-477
1d
PDEase_I-3ly2H04
H:233-477
1e
PDEase_I-3ly2H05
H:233-477
1f
PDEase_I-3ly2H06
H:233-477
1g
PDEase_I-3ly2H07
H:233-477
1h
PDEase_I-3ly2H08
H:233-477
[
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Atom Selection
(currently selected atoms:
all
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Protein
Nucleic
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Hetero
Ligand
Solvent
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Chain C
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Chain G
Chain H
Asymmetric Unit 1
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select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
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In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
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