![spacer](http://www.ebi.ac.uk/inc/images/spacer.gif) |
T5S : Summary
Code ![](/pdbe/static/images/help.png)
|
T5S
|
One-letter code ![](/pdbe/static/images/help.png)
|
T
|
Molecule name ![](/pdbe/static/images/help.png)
|
2'-deoxy-5-(methylselanyl)uridine 5'-phosphate
|
Systematic names ![](/pdbe/static/images/help.png)
|
|
Formula ![](/pdbe/static/images/help.png)
|
C10 H15 N2 O8 P Se
|
Formal charge ![](/pdbe/static/images/help.png)
|
0
|
Molecular weight ![](/pdbe/static/images/help.png)
|
401.168 Da
|
SMILES ![](/pdbe/static/images/help.png)
|
Type | Program | Version | Descriptor |
SMILES
|
ACDLabs |
10.04 |
O=P(O)(O)OCC2OC(N1C(=O)NC(=O)C([Se]C)=C1)CC2O |
SMILES
|
CACTVS |
3.341 |
C[Se]C1=CN([CH]2C[CH](O)[CH](CO[P](O)(O)=O)O2)C(=O)NC1=O |
SMILES
|
OpenEye OEToolkits |
1.5.0 |
C[Se]C1=CN(C(=O)NC1=O)C2CC(C(O2)COP(=O)(O)O)O |
Canonical SMILES
|
CACTVS |
3.341 |
C[Se]C1=CN([C@H]2C[C@H](O)[C@@H](CO[P](O)(O)=O)O2)C(=O)NC1=O |
Canonical SMILES
|
OpenEye OEToolkits |
1.5.0 |
C[Se]C1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O)O)O |
|
IUPAC InChI ![](/pdbe/static/images/help.png) | InChI=1S/C10H15N2O8PSe/c1-22-7-3-12(10(15)11-9(7)14)8-2-5(13)6(20-8)4-19-21(16,17)18/h3,5-6,8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t5-,6+,8+/m0/s1 |
IUPAC InChI key ![](/pdbe/static/images/help.png) | KJNLUXBKSKRISX-SHYZEUOFSA-N |
|
wwPDB Information |
Atom count ![](/pdbe/static/images/help.png)
|
37 (22 without Hydrogen)
|
Polymer type ![](/pdbe/static/images/help.png)
|
Deoxy ribonucleotide
|
Type description ![](/pdbe/static/images/help.png)
|
DNA LINKING
|
Type code ![](/pdbe/static/images/help.png)
|
ATOMN
|
Is modified ![](/pdbe/static/images/help.png)
|
Yes
|
Standard parent ![](/pdbe/static/images/help.png)
|
DT
|
Defined at ![](/pdbe/static/images/help.png)
|
2007-12-27
|
Last modified at ![](/pdbe/static/images/help.png)
|
2011-06-04
|
Status ![](/pdbe/static/images/help.png)
|
Released
|
Obsoleted ![](/pdbe/static/images/help.png)
|
Not Assigned
|
|
|
T5S : Atoms of Molecule
Total Number of Atoms: 37
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
OP3 |
O |
OP3 |
N |
N |
Y |
0 |
-5.438 |
2.545 |
-1.291 |
2 |
P |
P |
P |
N |
N |
N |
0 |
-5.374 |
1.298 |
-0.274 |
3 |
OP1 |
O |
OP1 |
N |
N |
N |
0 |
-5.276 |
1.799 |
1.115 |
4 |
OP2 |
O |
OP2 |
N |
N |
N |
0 |
-6.707 |
0.409 |
-0.431 |
5 |
O5' |
O |
O5' |
N |
N |
N |
0 |
-4.085 |
0.395 |
-0.612 |
6 |
N1 |
N |
N1 |
N |
N |
N |
0 |
1.025 |
-0.597 |
0.16 |
7 |
C6 |
C |
C6 |
N |
N |
N |
0 |
2.181 |
-0.499 |
-0.566 |
8 |
C2 |
C |
C2 |
N |
N |
N |
0 |
0.944 |
-0.067 |
1.394 |
9 |
O2 |
O |
O2 |
N |
N |
N |
0 |
-0.093 |
-0.166 |
2.022 |
10 |
N3 |
N |
N3 |
N |
N |
N |
0 |
1.994 |
0.57 |
1.944 |
11 |
C4 |
C |
C4 |
N |
N |
N |
0 |
3.151 |
0.688 |
1.261 |
12 |
O4 |
O |
O4 |
N |
N |
N |
0 |
4.102 |
1.265 |
1.757 |
13 |
C5 |
C |
C5 |
N |
N |
N |
0 |
3.25 |
0.134 |
-0.039 |
14 |
SE |
SE |
SE |
N |
N |
N |
0 |
4.917 |
0.287 |
-1.059 |
15 |
CH3 |
C |
CH3 |
N |
N |
N |
0 |
6.041 |
1.276 |
0.207 |
16 |
C2' |
C |
C2' |
N |
N |
N |
0 |
-0.471 |
-2.55 |
0.398 |
17 |
C5' |
C |
C5' |
N |
N |
N |
0 |
-3.692 |
-0.728 |
0.179 |
18 |
C4' |
C |
C4' |
R |
N |
N |
0 |
-2.432 |
-1.357 |
-0.417 |
19 |
O4' |
O |
O4' |
N |
N |
N |
0 |
-1.314 |
-0.45 |
-0.302 |
20 |
C1' |
C |
C1' |
R |
N |
N |
0 |
-0.137 |
-1.28 |
-0.415 |
21 |
C3' |
C |
C3' |
S |
N |
N |
0 |
-2.015 |
-2.602 |
0.396 |
22 |
O3' |
O |
O3' |
N |
N |
N |
0 |
-2.475 |
-3.795 |
-0.243 |
23 |
HOP3 |
H |
HOP3 |
N |
N |
N |
0 |
-6.191 |
3.133 |
-1.146 |
24 |
HOP2 |
H |
HOP2 |
N |
N |
N |
0 |
-6.837 |
0.047 |
-1.318 |
25 |
H6 |
H |
H6 |
N |
N |
N |
0 |
2.238 |
-0.928 |
-1.556 |
26 |
HN3 |
H |
HN3 |
N |
N |
N |
0 |
1.919 |
0.946 |
2.834 |
27 |
HH3 |
H |
HH3 |
N |
N |
N |
0 |
7.025 |
1.44 |
-0.232 |
28 |
HH3A |
H |
HH3A |
N |
N |
N |
0 |
5.577 |
2.237 |
0.43 |
29 |
HH3B |
H |
HH3B |
N |
N |
N |
0 |
6.144 |
0.701 |
1.127 |
30 |
H2' |
H |
H2' |
N |
N |
N |
0 |
-0.058 |
-3.434 |
-0.088 |
31 |
H2'A |
H |
H2'A |
N |
N |
N |
0 |
-0.091 |
-2.463 |
1.416 |
32 |
H5' |
H |
H5' |
N |
N |
N |
0 |
-3.487 |
-0.401 |
1.199 |
33 |
H5'A |
H |
H5'A |
N |
N |
N |
0 |
-4.496 |
-1.464 |
0.189 |
34 |
H4' |
H |
H4' |
N |
N |
N |
0 |
-2.599 |
-1.622 |
-1.461 |
35 |
H1' |
H |
H1' |
N |
N |
N |
0 |
0.049 |
-1.534 |
-1.458 |
36 |
H3' |
H |
H3' |
N |
N |
N |
0 |
-2.4 |
-2.54 |
1.414 |
37 |
HO3' |
H |
HO3' |
N |
N |
Y |
0 |
-2.19 |
-4.61 |
0.194 |
T5S : Chemical Bonds
Total Number of Bonds: 38
T5S : Used in PDB Entries
Total Number of PDB Entries: 6
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
T5S |
3bm0 ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724386878788) |
Polymer component
|
1 |
1 |
T5S |
3ltu ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724386878788) |
Polymer component
|
1 |
1 |
T5S |
4rhd ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724386878788) |
Polymer component
|
8 |
2 |
T5S |
5usa ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724386878788) |
Polymer component
|
1 |
1 |
T5S |
5use ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724386878788) |
Polymer component
|
1 |
1 |
T5S |
5usg ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724386878788) |
Polymer component
|
2 |
2 |
|