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3SL4
Biol. Unit 1
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
]
Hetero Components
(5, 21)
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
2
Ligand/Ion
DIMETHYL SULFOXIDE
2
EDO
16
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
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
6
PO4
1
Ligand/Ion
PHOSPHATE ION
7
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(28, 28)
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: DC3 (SOFTWARE)
25: EC5 (SOFTWARE)
26: FC8 (SOFTWARE)
27: GC7 (SOFTWARE)
28: HC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PO4 A:20 , HIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , HOH A:486
BINDING SITE FOR RESIDUE ZN A 1
02
AC2
SOFTWARE
PO4 A:20 , HOH A:54 , ASP A:201 , HOH A:486 , HOH A:490 , HOH A:529
BINDING SITE FOR RESIDUE ZN A 2
03
AC3
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH B:500 , HOH B:535
BINDING SITE FOR RESIDUE EDO A 4
04
AC4
SOFTWARE
GLU A:218 , LYS C:239
BINDING SITE FOR RESIDUE EDO A 5
05
AC5
SOFTWARE
PRO A:138 , ASP A:140 , THR A:141
BINDING SITE FOR RESIDUE DMS A 6
06
AC6
SOFTWARE
ARG A:350 , EDO C:8 , THR C:148 , ASP C:151
BINDING SITE FOR RESIDUE EDO A 7
07
AC7
SOFTWARE
ASP A:156 , ALA A:158 , PRO A:205 , GLU A:339 , ARG A:342 , ARG A:346 , HOH A:482
BINDING SITE FOR RESIDUE EDO A 9
08
AC8
SOFTWARE
LEU A:175 , THR A:178 , TRP A:384 , VAL A:388 , ILE A:395
BINDING SITE FOR RESIDUE EDO A 10
09
AC9
SOFTWARE
LEU A:132 , LYS A:136 , ILE A:137 , VAL A:139 , HOH A:471 , HOH A:478
BINDING SITE FOR RESIDUE EDO A 11
10
BC1
SOFTWARE
ASN A:115 , ARG A:116 , GLU A:150 , ASP A:151 , TYR A:153 , ASN A:162 , HOH A:542
BINDING SITE FOR RESIDUE PEG A 440
11
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
12
BC3
SOFTWARE
PHE A:238 , PHE A:249 , ARG A:257 , ARG A:261 , HOH A:536 , HOH A:539
BINDING SITE FOR RESIDUE EDO A 14
13
BC4
SOFTWARE
ASP A:266 , GLN A:311
BINDING SITE FOR RESIDUE EDO A 15
14
BC5
SOFTWARE
GLU A:218 , HIS C:152 , LYS C:239 , HOH C:479
BINDING SITE FOR RESIDUE EDO A 16
15
BC6
SOFTWARE
ASN A:115 , ALA A:155 , ASN A:162 , ILE A:163
BINDING SITE FOR RESIDUE EDO A 17
16
BC7
SOFTWARE
EDO A:13 , THR A:186 , LEU A:188 , SER A:259 , MET A:263
BINDING SITE FOR RESIDUE EDO A 18
17
BC8
SOFTWARE
ARG A:330 , GLU A:366 , THR A:409 , HOH A:463 , PRO B:411 , GLN B:412
BINDING SITE FOR RESIDUE EDO A 19
18
BC9
SOFTWARE
ZN A:1 , ZN A:2 , JN4 A:23 , HIS A:160 , HIS A:164 , ASP A:201 , ASP A:318 , HOH A:452 , HOH A:485 , HOH A:486
BINDING SITE FOR RESIDUE PO4 A 20
19
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
20
CC2
SOFTWARE
PO4 A:20 , TYR A:159 , LEU A:319 , ASN A:321 , PRO A:322 , TYR A:329 , THR A:333 , ILE A:336 , MET A:337 , MET A:357 , GLN A:369 , PHE A:372 , HOH A:444 , HOH A:485
BINDING SITE FOR RESIDUE JN4 A 23
21
CC3
SOFTWARE
GLN A:258 , EDO B:9 , GLN B:210 , ASN B:214
BINDING SITE FOR RESIDUE EDO A 441
22
CC4
SOFTWARE
HIS A:105 , VAL A:106 , PHE A:107 , ARG A:108 , GLN A:331
BINDING SITE FOR RESIDUE DMS A 442
23
CC5
SOFTWARE
THR A:148 , HIS A:152 , GLU A:243 , HOH A:462 , HOH C:73 , PHE C:211 , THR C:215 , ARG C:350
BINDING SITE FOR RESIDUE EDO A 443
24
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
25
EC5
SOFTWARE
EDO A:7 , HIS C:152 , GLU C:243
BINDING SITE FOR RESIDUE EDO C 8
26
FC8
SOFTWARE
ASP A:156 , GLU C:150 , ASP C:151 , TYR C:153
BINDING SITE FOR RESIDUE EDO C 14
27
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
28
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
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_068245 (T285P, chain A, )
2: VAR_069453 (E288A, chain A, )
3: VAR_069454 (G371D, chain A, )
4: VAR_069455 (I376T, chain A, )
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)
---
A
T
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
A
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
A
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
A
I
376
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A: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
A: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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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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Sorry, no Info available
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Asymmetric Unit 1
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Asym.Unit (244 KB)
Header - Asym.Unit
Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
Biol.Unit 2 (63 KB)
Header - Biol.Unit 2
Biol.Unit 3 (63 KB)
Header - Biol.Unit 3
Biol.Unit 4 (64 KB)
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