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.
5MAR
Asym. Unit
Info
Asym.Unit (321 KB)
Biol.Unit 1 (159 KB)
Biol.Unit 2 (159 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF HUMAN SIRT2 IN COMPLEX WITH 1,2,4-OXADIAZOLE INHIBITOR AND ADP RIBOSE.
Authors
:
S. Moniot, C. Steegborn
Date
:
04 Nov 16 (Deposition) - 15 Mar 17 (Release) - 05 Apr 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.89
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Sirtuin, Nad-Dependent Protein Deacylase, Inhibitor Complex, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Moniot, M. Forgione, A. Lucidi, G. S. Hailu, A. Nebbioso, V. Carafa, F. Baratta, L. Altucci, N. Giacche, D. Passeri, R. Pellicciari, A. Mai C. Steegborn, D. Rotili
Development Of 1, 2, 4-Oxadiazoles As Potent And Selective Inhibitors Of The Human Deacetylase Sirtuin 2: Structure-Activity Relationship, X-Ray Crystal Structure, And Anticancer Activity.
J. Med. Chem. V. 60 2344 2017
[
close entry info
]
Hetero Components
(7, 22)
Info
All Hetero Components
1a: 3-[3-(4-CHLOROPHENYL)-1,2,4-OXADIA... (7KEa)
1b: 3-[3-(4-CHLOROPHENYL)-1,2,4-OXADIA... (7KEb)
2a: ACETATE ION (ACTa)
3a: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-Y... (AR6a)
3b: [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-Y... (AR6b)
4a: DIMETHYL SULFOXIDE (DMSa)
4b: DIMETHYL SULFOXIDE (DMSb)
4c: DIMETHYL SULFOXIDE (DMSc)
4d: DIMETHYL SULFOXIDE (DMSd)
4e: DIMETHYL SULFOXIDE (DMSe)
4f: DIMETHYL SULFOXIDE (DMSf)
4g: DIMETHYL SULFOXIDE (DMSg)
4h: DIMETHYL SULFOXIDE (DMSh)
4i: DIMETHYL SULFOXIDE (DMSi)
5a: 1,2-ETHANEDIOL (EDOa)
5b: 1,2-ETHANEDIOL (EDOb)
6a: GLYCEROL (GOLa)
6b: GLYCEROL (GOLb)
6c: GLYCEROL (GOLc)
6d: GLYCEROL (GOLd)
7a: ZINC ION (ZNa)
7b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
7KE
2
Ligand/Ion
3-[3-(4-CHLOROPHENYL)-1,2,4-OXADIAZOL-5-YL]PROPAN-1-OL
2
ACT
1
Ligand/Ion
ACETATE ION
3
AR6
2
Ligand/Ion
[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGENPHOSPHATE
4
DMS
9
Ligand/Ion
DIMETHYL SULFOXIDE
5
EDO
2
Ligand/Ion
1,2-ETHANEDIOL
6
GOL
4
Ligand/Ion
GLYCEROL
7
ZN
2
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: 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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:195 , CYS A:200 , CYS A:221 , CYS A:224
binding site for residue ZN A 401
02
AC2
SOFTWARE
GLY A:84 , ALA A:85 , GLY A:86 , THR A:89 , ASP A:95 , PHE A:96 , ARG A:97 , TYR A:104 , GLN A:167 , HIS A:187 , PHE A:235 , GLY A:261 , THR A:262 , SER A:263 , VAL A:266 , ASN A:286 , LYS A:287 , GLU A:288 , GLY A:322 , GLU A:323 , CYS A:324 , 7KE A:403 , EDO A:405 , HOH A:535 , HOH A:545 , HOH A:554 , HOH A:606
binding site for residue AR6 A 402
03
AC3
SOFTWARE
PHE A:96 , PHE A:119 , LEU A:134 , LEU A:138 , ILE A:169 , ILE A:232 , VAL A:233 , AR6 A:402 , LEU B:297
binding site for residue 7KE A 403
04
AC4
SOFTWARE
SER A:311 , ALA A:314
binding site for residue EDO A 404
05
AC5
SOFTWARE
THR A:89 , SER A:90 , LYS A:287 , GLU A:323 , AR6 A:402
binding site for residue EDO A 405
06
AC6
SOFTWARE
TRP A:320 , LEU A:321
binding site for residue DMS A 406
07
AC7
SOFTWARE
PHE A:96 , ASN A:168 , ILE A:169 , ASP A:170
binding site for residue DMS A 407
08
AC8
SOFTWARE
ARG A:77 , ARG A:78 , GLY A:159 , LEU A:161 , LEU A:162
binding site for residue DMS A 408
09
AC9
SOFTWARE
LEU A:162 , ARG A:163 , GLU A:181 , ASP A:182
binding site for residue DMS A 409
10
AD1
SOFTWARE
ARG A:75 , TYR A:104 , ASP A:105
binding site for residue DMS A 410
11
AD2
SOFTWARE
GLY A:291 , SER A:293 , MET A:299 , MET A:301 , GLY A:302 , GLY A:304 , GLY A:305 , GLY A:306 , HOH A:559
binding site for residue GOL A 411
12
AD3
SOFTWARE
ARG A:153 , GLU A:348 , SER A:351 , HOH A:507 , CYS B:224
binding site for residue GOL A 412
13
AD4
SOFTWARE
CYS B:195 , CYS B:200 , CYS B:221 , CYS B:224
binding site for residue ZN B 401
14
AD5
SOFTWARE
GLY B:84 , ALA B:85 , GLY B:86 , THR B:89 , ASP B:95 , PHE B:96 , ARG B:97 , TYR B:104 , GLN B:167 , HIS B:187 , PHE B:235 , GLY B:261 , THR B:262 , SER B:263 , VAL B:266 , ASN B:286 , LYS B:287 , GLU B:288 , GLY B:322 , GLU B:323 , CYS B:324 , 7KE B:403 , HOH B:533 , HOH B:547 , HOH B:548
binding site for residue AR6 B 402
15
AD6
SOFTWARE
PHE B:96 , PHE B:119 , LEU B:134 , LEU B:138 , ILE B:169 , ILE B:232 , VAL B:233 , AR6 B:402
binding site for residue 7KE B 403
16
AD7
SOFTWARE
ALA B:319 , TRP B:320 , LEU B:321
binding site for residue ACT B 404
17
AD8
SOFTWARE
PHE B:96 , ASN B:168 , ILE B:169 , ASP B:170
binding site for residue DMS B 405
18
AD9
SOFTWARE
ARG B:77 , GLY B:159 , LEU B:161
binding site for residue DMS B 406
19
AE1
SOFTWARE
LEU B:162 , ARG B:163 , GLU B:181 , ASP B:182
binding site for residue DMS B 407
20
AE2
SOFTWARE
HOH A:556 , HOH A:701 , TYR B:114 , GOL B:409
binding site for residue DMS B 408
21
AE3
SOFTWARE
GLU B:116 , DMS B:408
binding site for residue GOL B 409
22
AE4
SOFTWARE
SER A:73 , GLU A:74 , CYS A:76 , ARG A:77 , SER B:122 , TYR B:123 , LYS B:126 , HOH B:558 , HOH B:598
binding site for residue GOL B 410
[
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 (321 KB)
Header - Asym.Unit
Biol.Unit 1 (159 KB)
Header - Biol.Unit 1
Biol.Unit 2 (159 KB)
Header - Biol.Unit 2
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
5MAR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help