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.
5KOT
Asym. Unit
Info
Asym.Unit (232 KB)
Biol.Unit 1 (114 KB)
Biol.Unit 2 (114 KB)
Biol.Unit 3 (661 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DISCOVERY OF TAK-272: A NOVEL, POTENT AND ORALLY ACTIVE RENIN IN-HIBITOR
Authors
:
G. P. Snell, C. A. Behnke, K. Okada, O. Hideyuki, B. -C. Sang, W. Lane
Date
:
01 Jul 16 (Deposition) - 05 Jul 17 (Release) - 05 Jul 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (3x)
Keywords
:
Protein-Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Imaeda, H. Tokuhara, Y. Fukase, R. Kanagawa, Y. Kajimoto, K. Kusumoto, M. Kondo, G. P. Snell, C. A. Behnke, T. Kuroita
Discovery Of Tak-272: A Novel, Potent And Orally Active Renin Inhibitor
To Be Published
[
close entry info
]
Hetero Components
(5, 24)
Info
All Hetero Components
1a: 1-(4-METHOXYBUTYL)-~{N}-(2-METHYLP... (6VUa)
1b: 1-(4-METHOXYBUTYL)-~{N}-(2-METHYLP... (6VUb)
2a: DIMETHYL SULFOXIDE (DMSa)
2b: DIMETHYL SULFOXIDE (DMSb)
2c: DIMETHYL SULFOXIDE (DMSc)
2d: DIMETHYL SULFOXIDE (DMSd)
2e: DIMETHYL SULFOXIDE (DMSe)
2f: DIMETHYL SULFOXIDE (DMSf)
2g: DIMETHYL SULFOXIDE (DMSg)
2h: DIMETHYL SULFOXIDE (DMSh)
2i: DIMETHYL SULFOXIDE (DMSi)
2j: DIMETHYL SULFOXIDE (DMSj)
2k: DIMETHYL SULFOXIDE (DMSk)
2l: DIMETHYL SULFOXIDE (DMSl)
2m: DIMETHYL SULFOXIDE (DMSm)
2n: DIMETHYL SULFOXIDE (DMSn)
3a: N-ACETYL-D-GLUCOSAMINE (NAGa)
3b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
4d: DI(HYDROXYETHYL)ETHER (PEGd)
5a: TRIETHYLENE GLYCOL (PGEa)
5b: TRIETHYLENE GLYCOL (PGEb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6VU
2
Ligand/Ion
1-(4-METHOXYBUTYL)-~{N}-(2-METHYLPROPYL)-~{N}-[(3~{S},5~{R})-5-MORPHOLIN-4-YLCARBONYLPIPERIDIN-3-YL]BENZIMIDAZOLE-2-CARBOXAMIDE
2
DMS
14
Ligand/Ion
DIMETHYL SULFOXIDE
3
NAG
2
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
4
PEG
4
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PGE
2
Ligand/Ion
TRIETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(23, 23)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:18 , GLN A:19 , TYR A:20 , VAL A:36 , ASP A:38 , GLY A:40 , TYR A:83 , SER A:84 , THR A:85 , PRO A:118 , PHE A:124 , VAL A:127 , LEU A:224 , ASP A:226 , THR A:227 , GLY A:228 , SER A:230 , THR A:309 , DMS A:411 , HOH A:537
binding site for residue 6VU A 402
02
AC2
SOFTWARE
ASN A:189 , HIS A:191 , LYS A:275 , GLU A:276 , TYR A:277 , PHE A:336 , DMS A:414 , HOH A:519
binding site for residue PGE A 403
03
AC3
SOFTWARE
LYS A:197 , LEU B:54
binding site for residue PEG A 405
04
AC4
SOFTWARE
GLY A:211 , SER A:212 , THR A:214 , GLU A:276
binding site for residue PEG A 406
05
AC5
SOFTWARE
ASP A:17 , ALA A:282 , ASP A:283 , VAL A:285 , PHE A:286 , ARG A:321
binding site for residue DMS A 407
06
AC6
SOFTWARE
VAL A:59 , TYR A:60 , SER A:84 , MET A:303 , ASP A:304
binding site for residue DMS A 408
07
AC7
SOFTWARE
ARG A:251 , LEU A:252 , PHE A:253 , ASP A:254 , TYR A:255 , HIS A:301 , ALA A:302 , HOH A:615
binding site for residue DMS A 409
08
AC8
SOFTWARE
HIS A:61 , MET A:120 , ALA A:122 , LEU A:252
binding site for residue DMS A 410
09
AC9
SOFTWARE
SER A:84 , ASP A:226 , MET A:303 , ALA A:314 , 6VU A:402
binding site for residue DMS A 411
10
AD1
SOFTWARE
SER A:70 , TYR A:72 , LYS A:73 , GLU B:155 , VAL B:157 , ASP B:328 , HOH B:541
binding site for residue DMS A 412
11
AD2
SOFTWARE
LEU A:79 , LEU A:81 , PHE A:91 , GLY A:109 , VAL A:111 , HOH A:589
binding site for residue DMS A 413
12
AD3
SOFTWARE
GLY A:188 , ASN A:189 , PGE A:403 , THR B:98 , GLY B:100
binding site for residue DMS A 414
13
AD4
SOFTWARE
THR B:18 , GLN B:19 , TYR B:20 , VAL B:36 , ASP B:38 , GLY B:40 , TYR B:83 , SER B:84 , THR B:85 , PRO B:118 , VAL B:127 , LEU B:224 , ASP B:226 , THR B:227 , GLY B:228 , ALA B:229 , SER B:230 , ILE B:305 , THR B:309 , DMS B:405 , DMS B:410 , HOH B:553
binding site for residue 6VU B 402
14
AD5
SOFTWARE
HIS A:74 , LEU B:195 , ILE B:196 , LYS B:197 , ARG B:330 , ASN B:331 , ASN B:332 , HOH B:558
binding site for residue PGE B 403
15
AD6
SOFTWARE
THR B:85 , LEU B:121 , HIS B:301 , HOH B:511
binding site for residue PEG B 404
16
AD7
SOFTWARE
SER B:84 , ASP B:226 , ALA B:314 , 6VU B:402
binding site for residue DMS B 405
17
AD8
SOFTWARE
THR B:18 , GLN B:19 , SER B:230 , ASN B:260
binding site for residue DMS B 406
18
AD9
SOFTWARE
GLU B:276 , TYR B:277 , PHE B:323 , HOH B:556
binding site for residue DMS B 407
19
AE1
SOFTWARE
LEU B:79 , LEU B:81 , GLY B:90 , PHE B:91 , GLY B:109 , VAL B:111 , HOH B:520
binding site for residue DMS B 408
20
AE2
SOFTWARE
GLU A:187 , ILE B:11 , HOH B:542
binding site for residue DMS B 409
21
AE3
SOFTWARE
SER B:41 , ARG B:82 , ILE B:137 , 6VU B:402
binding site for residue DMS B 410
22
AE4
SOFTWARE
ASN A:75 , HOH A:517 , HOH A:527
binding site for Mono-Saccharide NAG A 401 bound to ASN A 75
23
AE5
SOFTWARE
ASN B:75 , THR B:77 , MET B:107 , HOH B:537 , HOH B:599
binding site for Mono-Saccharide NAG B 401 bound to ASN B 75
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain B
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 (232 KB)
Header - Asym.Unit
Biol.Unit 1 (114 KB)
Header - Biol.Unit 1
Biol.Unit 2 (114 KB)
Header - Biol.Unit 2
Biol.Unit 3 (661 KB)
Header - Biol.Unit 3
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
5KOT
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
