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3LY2
Biol. Unit 4
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
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Hetero Components
(1, 1)
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:
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Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
SO4
-1
Ligand/Ion
SULFATE ION
3
Z72
1
Ligand/Ion
8-(CYCLOPENTYLOXY)-4-[(3,5-DICHLOROPYRIDIN-4-YL)AMINO]-7-METHOXY-2H-CHROMEN-2-ONE
4
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(3, 3)
Info
All Sites
1: BC3 (SOFTWARE)
2: BC4 (SOFTWARE)
3: BC5 (SOFTWARE)
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Label:
No.
Name
Evidence
Residues
Description
1
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
2
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
3
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
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (D:274-285)
;
View:
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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
1
-
-
-
D:274-285
-
-
-
-
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Exons
(0, 0)
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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, 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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(
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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)
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all CATH domains
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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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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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Asymmetric Unit 1
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Asym.Unit (458 KB)
Header - Asym.Unit
Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
Biol.Unit 2 (64 KB)
Header - Biol.Unit 2
Biol.Unit 3 (62 KB)
Header - Biol.Unit 3
Biol.Unit 4 (62 KB)
Header - Biol.Unit 4
Biol.Unit 5 (61 KB)
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Biol.Unit 6 (61 KB)
Header - Biol.Unit 6
Biol.Unit 7 (62 KB)
Header - Biol.Unit 7
Biol.Unit 8 (62 KB)
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