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DX : Summary
Code
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DX
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One-letter code
|
X
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Molecule name
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[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)imidazo[1,2-a][1,3,5]triazin-8-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate
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Systematic names
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Formula
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C10 H13 N4 O8 P
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Formal charge
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0
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Molecular weight
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348.206 Da
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SMILES
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Type | Program | Version | Descriptor |
SMILES
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CACTVS |
3.385 |
O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CN3C(=O)NC(=O)N=C23 |
SMILES
|
OpenEye OEToolkits |
2.0.5 |
C1C(C(OC1N2C=CN3C2=NC(=O)NC3=O)COP(=O)(O)O)O |
Canonical SMILES
|
CACTVS |
3.385 |
O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CN3C(=O)NC(=O)N=C23 |
Canonical SMILES
|
OpenEye OEToolkits |
2.0.5 |
C1[C@@H]([C@H](O[C@H]1N2C=CN3C2=NC(=O)NC3=O)COP(=O)(O)O)O |
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IUPAC InChI | InChI=1S/C10H13N4O8P/c15-5-3-7(22-6(5)4-21-23(18,19)20)13-1-2-14-9(13)11-8(16)12-10(14)17/h1-2,5-7,15H,3-4H2,(H,12,16,17)(H2,18,19,20)/t5-,6+,7+/m0/s1 |
IUPAC InChI key | MIJXVMWIKXUKNK-RRKCRQDMSA-N |
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wwPDB Information |
Atom count
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36 (23 without Hydrogen)
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Polymer type
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Deoxy ribonucleotide
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Type description
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DNA linking
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Type code
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ATOMN
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Is modified
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No
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Standard parent
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Not Assigned
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Defined at
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2016-07-19
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Last modified at
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2018-03-02
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Status
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Released
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Obsoleted
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Not Assigned
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DX : Atoms of Molecule
Total Number of Atoms: 36
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
P |
P |
P1 |
N |
N |
N |
0 |
4.861 |
-1.083 |
-0.285 |
2 |
OP1 |
O |
O1 |
N |
N |
N |
0 |
4.848 |
-1.705 |
1.058 |
3 |
O5' |
O |
O2 |
N |
N |
N |
0 |
3.488 |
-0.274 |
-0.515 |
4 |
C5' |
C |
C1 |
N |
N |
N |
0 |
3.023 |
0.74 |
0.378 |
5 |
C4' |
C |
C2 |
R |
N |
N |
0 |
1.695 |
1.301 |
-0.135 |
6 |
C3' |
C |
C3 |
S |
N |
N |
0 |
1.216 |
2.459 |
0.768 |
7 |
O3' |
O |
O3 |
N |
N |
N |
0 |
1.557 |
3.72 |
0.189 |
8 |
C2' |
C |
C4 |
N |
N |
N |
0 |
-0.318 |
2.285 |
0.82 |
9 |
C1' |
C |
C5 |
R |
N |
N |
0 |
-0.585 |
1.042 |
-0.058 |
10 |
O4' |
O |
O4 |
N |
N |
N |
0 |
0.657 |
0.302 |
-0.04 |
11 |
N9 |
N |
N1 |
N |
N |
N |
0 |
-1.667 |
0.237 |
0.513 |
12 |
C4 |
C |
C6 |
N |
N |
N |
0 |
-2.879 |
0.007 |
-0.058 |
13 |
N5 |
N |
N2 |
N |
N |
N |
0 |
-3.59 |
-0.792 |
0.791 |
14 |
C7 |
C |
C7 |
N |
N |
N |
0 |
-2.795 |
-1.051 |
1.896 |
15 |
C8 |
C |
C8 |
N |
N |
N |
0 |
-1.633 |
-0.429 |
1.726 |
16 |
N3 |
N |
N3 |
N |
N |
N |
0 |
-3.417 |
0.405 |
-1.202 |
17 |
C2 |
C |
C9 |
N |
N |
N |
0 |
-4.655 |
0.03 |
-1.533 |
18 |
O2 |
O |
O5 |
N |
N |
N |
0 |
-5.138 |
0.402 |
-2.588 |
19 |
N1 |
N |
N4 |
N |
N |
N |
0 |
-5.372 |
-0.759 |
-0.71 |
20 |
C6 |
C |
C10 |
N |
N |
N |
0 |
-4.84 |
-1.173 |
0.458 |
21 |
O6 |
O |
O6 |
N |
N |
N |
0 |
-5.482 |
-1.885 |
1.206 |
22 |
OP2 |
O |
O7 |
N |
N |
N |
0 |
6.106 |
-0.069 |
-0.395 |
23 |
H2 |
H |
H2 |
N |
N |
N |
0 |
2.878 |
0.312 |
1.37 |
24 |
H3 |
H |
H3 |
N |
N |
N |
0 |
3.759 |
1.541 |
0.433 |
25 |
H4 |
H |
H4 |
N |
N |
N |
0 |
1.801 |
1.642 |
-1.165 |
26 |
H5 |
H |
H5 |
N |
N |
N |
0 |
1.647 |
2.369 |
1.765 |
27 |
H6 |
H |
H6 |
N |
N |
N |
0 |
1.28 |
4.483 |
0.715 |
28 |
H7 |
H |
H7 |
N |
N |
N |
0 |
-0.647 |
2.106 |
1.844 |
29 |
H8 |
H |
H8 |
N |
N |
N |
0 |
-0.818 |
3.16 |
0.405 |
30 |
H9 |
H |
H9 |
N |
N |
N |
0 |
-0.831 |
1.342 |
-1.076 |
31 |
H10 |
H |
H10 |
N |
N |
N |
0 |
-3.072 |
-1.655 |
2.747 |
32 |
H11 |
H |
H11 |
N |
N |
N |
0 |
-0.802 |
-0.444 |
2.416 |
33 |
H13 |
H |
H13 |
N |
N |
N |
0 |
-6.271 |
-1.028 |
-0.956 |
34 |
H14 |
H |
H14 |
N |
N |
N |
0 |
6.177 |
0.376 |
-1.25 |
35 |
OP3 |
O |
O8 |
N |
N |
Y |
0 |
5.003 |
-2.23 |
-1.406 |
36 |
H1 |
H |
H1 |
N |
N |
N |
0 |
5.809 |
-2.759 |
-1.328 |
DX : Chemical Bonds
Total Number of Bonds: 38
DX : Used in PDB Entries
Total Number of PDB Entries: 1
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
DX |
5vbs |
Polymer component
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2 |
2 |
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