PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
4KP6
Asym. Unit
Info
Asym.Unit (123 KB)
Biol.Unit 1 (117 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4B (PDE4B) IN COMPLEX WITH A [1,3,5]TRIAZINE DERIVATIVE
Authors
:
R. Gewald, C. Grunwald, U. Egerland
Date
:
13 May 13 (Deposition) - 10 Jul 13 (Release) - 17 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.50
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Pde4 Inhibitor, Phosphodiesterase, Triazine, Neutrophilia, Copd, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Gewald, C. Grunwald, U. Egerland
Discovery Of Triazines As Potent, Selective And Orally Active Pde4 Inhibitors.
Bioorg. Med. Chem. Lett. V. 23 4308 2013
[
close entry info
]
Hetero Components
(4, 22)
Info
All Hetero Components
1a: 2-ETHYL-2-{[4-(METHYLAMINO)-6-(1H-... (1S1a)
2a: 1,2-ETHANEDIOL (EDOa)
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)
3a: MAGNESIUM ION (MGa)
4a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1S1
1
Ligand/Ion
2-ETHYL-2-{[4-(METHYLAMINO)-6-(1H-1,2,4-TRIAZOL-1-YL)-1,3,5-TRIAZIN-2-YL]AMINO}BUTANENITRILE
2
EDO
19
Ligand/Ion
1,2-ETHANEDIOL
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:234 , MET A:347 , ASN A:395 , THR A:407 , ILE A:410 , MET A:431 , SER A:442 , GLN A:443 , PHE A:446 , HOH A:635 , HOH A:646
BINDING SITE FOR RESIDUE 1S1 A 501
02
AC2
SOFTWARE
ASP A:275 , HOH A:612 , HOH A:613 , HOH A:709 , HOH A:712 , HOH A:726
BINDING SITE FOR RESIDUE MG A 502
03
AC3
SOFTWARE
HIS A:238 , HIS A:274 , ASP A:275 , ASP A:392 , HOH A:711 , HOH A:712
BINDING SITE FOR RESIDUE ZN A 503
04
AC4
SOFTWARE
THR A:208 , PHE A:209 , ASN A:325 , LEU A:326 , GLN A:330 , EDO A:521
BINDING SITE FOR RESIDUE EDO A 504
05
AC5
SOFTWARE
ARG A:210 , ILE A:211 , SER A:212 , THR A:215 , ASP A:321 , ILE A:322 , MET A:324 , ASN A:325 , EDO A:514 , HOH A:605
BINDING SITE FOR RESIDUE EDO A 505
06
AC6
SOFTWARE
ASN A:283 , ASP A:299 , SER A:301 , VAL A:302 , ASP A:346 , SER A:348 , EDO A:522
BINDING SITE FOR RESIDUE EDO A 506
07
AC7
SOFTWARE
GLY A:177 , LEU A:178 , ILE A:180 , ASP A:241 , LYS A:398 , LEU A:402 , TRP A:406 , HOH A:611
BINDING SITE FOR RESIDUE EDO A 507
08
AC8
SOFTWARE
SER A:251 , PRO A:253 , ASP A:256 , HOH A:669
BINDING SITE FOR RESIDUE EDO A 508
09
AC9
SOFTWARE
LEU A:249 , THR A:252 , TRP A:458 , ASP A:465
BINDING SITE FOR RESIDUE EDO A 509
10
BC1
SOFTWARE
ASP A:340 , LYS A:349 , ARG A:385
BINDING SITE FOR RESIDUE EDO A 510
11
BC2
SOFTWARE
TYR A:297 , HIS A:306 , ALA A:309
BINDING SITE FOR RESIDUE EDO A 511
12
BC3
SOFTWARE
HIS A:234 , GLY A:280 , GLU A:413 , PHE A:414 , GLN A:417 , EDO A:518 , HOH A:625
BINDING SITE FOR RESIDUE EDO A 512
13
BC4
SOFTWARE
SER A:212 , HOH A:647 , HOH A:671
BINDING SITE FOR RESIDUE EDO A 513
14
BC5
SOFTWARE
SER A:212 , ASP A:214 , THR A:215 , HIS A:319 , EDO A:505
BINDING SITE FOR RESIDUE EDO A 514
15
BC6
SOFTWARE
ARG A:331 , ARG A:335 , EDO A:516
BINDING SITE FOR RESIDUE EDO A 515
16
BC7
SOFTWARE
ASP A:321 , ARG A:331 , ARG A:335 , EDO A:515 , HOH A:653
BINDING SITE FOR RESIDUE EDO A 516
17
BC8
SOFTWARE
ASN A:174 , GLU A:202 , HIS A:247 , SER A:251
BINDING SITE FOR RESIDUE EDO A 517
18
BC9
SOFTWARE
SER A:282 , PRO A:430 , CYS A:432 , EDO A:512 , HOH A:693 , HOH A:710
BINDING SITE FOR RESIDUE EDO A 518
19
CC1
SOFTWARE
LEU A:250 , LEU A:255 , ALA A:257 , VAL A:258 , PHE A:259
BINDING SITE FOR RESIDUE EDO A 519
20
CC2
SOFTWARE
ARG A:203 , ASP A:204 , LEU A:205 , THR A:208 , ASP A:261 , ILE A:264 , HOH A:609
BINDING SITE FOR RESIDUE EDO A 520
21
CC3
SOFTWARE
THR A:208 , ASP A:261 , GLN A:330 , EDO A:504 , HOH A:746
BINDING SITE FOR RESIDUE EDO A 521
22
CC4
SOFTWARE
GLU A:300 , ASP A:346 , LYS A:349 , EDO A:506
BINDING SITE FOR RESIDUE EDO A 522
[
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
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d4kp6a_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d4kp6a_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
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)
[
close Script example commands
]
Log
Note:
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") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (123 KB)
Header - Asym.Unit
Biol.Unit 1 (117 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
4KP6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help