|
42E : Summary
Code
|
42E
|
One-letter code
|
X
|
Molecule name
|
[(2R,5S)-5-(4-amino-2-oxopyrimidin-1(2H)-yl)-1,3-oxathiolan-2-yl]methyl dihydrogen phosphate
|
Systematic names
|
|
Formula
|
C8 H12 N3 O6 P S
|
Formal charge
|
0
|
Molecular weight
|
309.236 Da
|
SMILES
|
Type | Program | Version | Descriptor |
SMILES
|
ACDLabs |
12.01 |
O=P(O)(O)OCC2OC(N1C(=O)N=C(N)C=C1)CS2 |
SMILES
|
CACTVS |
3.385 |
NC1=NC(=O)N(C=C1)[CH]2CS[CH](CO[P](O)(O)=O)O2 |
SMILES
|
OpenEye OEToolkits |
1.7.6 |
C1C(OC(S1)COP(=O)(O)O)N2C=CC(=NC2=O)N |
Canonical SMILES
|
CACTVS |
3.385 |
NC1=NC(=O)N(C=C1)[C@@H]2CS[C@H](CO[P](O)(O)=O)O2 |
Canonical SMILES
|
OpenEye OEToolkits |
1.7.6 |
C1[C@H](O[C@H](S1)COP(=O)(O)O)N2C=CC(=NC2=O)N |
|
IUPAC InChI | InChI=1S/C8H12N3O6PS/c9-5-1-2-11(8(12)10-5)6-4-19-7(17-6)3-16-18(13,14)15/h1-2,6-7H,3-4H2,(H2,9,10,12)(H2,13,14,15)/t6-,7+/m0/s1 |
IUPAC InChI key | WUMZLKDCOINBEA-NKWVEPMBSA-N |
|
wwPDB Information |
Atom count
|
31 (19 without Hydrogen)
|
Polymer type
|
Bound ligand
|
Type description
|
NON-POLYMER
|
Type code
|
HETAIN
|
Is modified
|
No
|
Standard parent
|
Not Assigned
|
Defined at
|
2015-01-29
|
Last modified at
|
2020-06-17
|
Status
|
Released
|
Obsoleted
|
Not Assigned
|
|
|
42E : Atoms of Molecule
Total Number of Atoms: 31
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
PA |
P |
PA |
N |
N |
N |
0 |
3.118 |
-0.976 |
-0.094 |
2 |
O1A |
O |
O1A |
N |
N |
N |
0 |
3.671 |
-1.284 |
1.244 |
3 |
O2A |
O |
O2A |
N |
N |
N |
0 |
2.497 |
-2.314 |
-0.739 |
4 |
O5' |
O |
O5' |
N |
N |
N |
0 |
1.964 |
0.138 |
0.046 |
5 |
C5' |
C |
C5' |
N |
N |
N |
0 |
2.174 |
1.401 |
0.679 |
6 |
C4' |
C |
C4' |
R |
N |
N |
0 |
0.879 |
2.214 |
0.639 |
7 |
O4' |
O |
O4' |
N |
N |
N |
0 |
-0.18 |
1.521 |
1.325 |
8 |
S3' |
S |
S3' |
N |
N |
N |
0 |
0.234 |
2.331 |
-1.082 |
9 |
C2' |
C |
C2' |
N |
N |
N |
0 |
-1.52 |
2.47 |
-0.533 |
10 |
C1' |
C |
C1' |
S |
N |
N |
0 |
-1.479 |
1.634 |
0.769 |
11 |
N1 |
N |
N1 |
N |
N |
N |
0 |
-1.985 |
0.29 |
0.48 |
12 |
C2 |
C |
C2 |
N |
N |
N |
0 |
-3.197 |
0.138 |
-0.085 |
13 |
O2 |
O |
O2 |
N |
N |
N |
0 |
-3.863 |
1.125 |
-0.35 |
14 |
N3 |
N |
N3 |
N |
N |
N |
0 |
-3.681 |
-1.072 |
-0.358 |
15 |
C4 |
C |
C4 |
N |
N |
N |
0 |
-2.978 |
-2.162 |
-0.08 |
16 |
N4 |
N |
N4 |
N |
N |
N |
0 |
-3.488 |
-3.407 |
-0.367 |
17 |
C5 |
C |
C5 |
N |
N |
N |
0 |
-1.704 |
-2.037 |
0.513 |
18 |
C6 |
C |
C6 |
N |
N |
N |
0 |
-1.224 |
-0.799 |
0.779 |
19 |
H2 |
H |
H2 |
N |
N |
N |
0 |
3.137 |
-3.03 |
-0.853 |
20 |
H3 |
H |
H3 |
N |
N |
N |
0 |
2.472 |
1.242 |
1.716 |
21 |
H4 |
H |
H4 |
N |
N |
N |
0 |
2.961 |
1.944 |
0.155 |
22 |
H5 |
H |
H5 |
N |
N |
N |
0 |
1.033 |
3.205 |
1.066 |
23 |
H6 |
H |
H6 |
N |
N |
N |
0 |
-1.787 |
3.507 |
-0.327 |
24 |
H7 |
H |
H7 |
N |
N |
N |
0 |
-2.198 |
2.029 |
-1.263 |
25 |
H8 |
H |
H8 |
N |
N |
N |
0 |
-2.135 |
2.1 |
1.504 |
26 |
H9 |
H |
H9 |
N |
N |
N |
0 |
-4.364 |
-3.489 |
-0.775 |
27 |
H10 |
H |
H10 |
N |
N |
N |
0 |
-2.971 |
-4.201 |
-0.162 |
28 |
H11 |
H |
H11 |
N |
N |
N |
0 |
-1.118 |
-2.914 |
0.742 |
29 |
H12 |
H |
H12 |
N |
N |
N |
0 |
-0.251 |
-0.678 |
1.232 |
30 |
OP3 |
O |
OP3 |
N |
N |
Y |
0 |
4.292 |
-0.417 |
-1.044 |
31 |
H1 |
H |
H1 |
N |
N |
Y |
0 |
4.001 |
-0.194 |
-1.938 |
42E : Chemical Bonds
Total Number of Bonds: 32
42E : Used in PDB Entries
Total Number of PDB Entries: 2
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
42E |
5tba |
Bound ligand
|
1 |
1 |
42E |
5tbc |
Bound ligand
|
1 |
1 |
|