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M1G : Summary
Code ![](/pdbe/static/images/help.png)
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M1G
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One-letter code ![](/pdbe/static/images/help.png)
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G
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Molecule name ![](/pdbe/static/images/help.png)
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3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5'-MONOPHOSPHATE
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Systematic names ![](/pdbe/static/images/help.png)
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Formula ![](/pdbe/static/images/help.png)
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C13 H14 N5 O7 P
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Formal charge ![](/pdbe/static/images/help.png)
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0
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Molecular weight ![](/pdbe/static/images/help.png)
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383.253 Da
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SMILES ![](/pdbe/static/images/help.png)
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Type | Program | Version | Descriptor |
SMILES
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ACDLabs |
10.04 |
O=C2c3ncn(c3N=C1N=CC=CN12)C4OC(C(O)C4)COP(=O)(O)O |
SMILES
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CACTVS |
3.341 |
O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=O)N4C=CC=NC4=Nc23 |
SMILES
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OpenEye OEToolkits |
1.5.0 |
c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C4N=CC=CN4C2=O |
Canonical SMILES
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CACTVS |
3.341 |
O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3C(=O)N4C=CC=NC4=Nc23 |
Canonical SMILES
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OpenEye OEToolkits |
1.5.0 |
c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)N=C4N=CC=CN4C2=O |
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IUPAC InChI ![](/pdbe/static/images/help.png) | InChI=1S/C13H14N5O7P/c19-7-4-9(25-8(7)5-24-26(21,22)23)18-6-15-10-11(18)16-13-14-2-1-3-17(13)12(10)20/h1-3,6-9,19H,4-5H2,(H2,21,22,23)/t7-,8+,9+/m0/s1 |
IUPAC InChI key ![](/pdbe/static/images/help.png) | VHESJINRMVWRRK-DJLDLDEBSA-N |
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wwPDB Information |
Atom count ![](/pdbe/static/images/help.png)
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40 (26 without Hydrogen)
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Polymer type ![](/pdbe/static/images/help.png)
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Deoxy ribonucleotide
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Type description ![](/pdbe/static/images/help.png)
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DNA LINKING
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Type code ![](/pdbe/static/images/help.png)
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ATOMN
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Is modified ![](/pdbe/static/images/help.png)
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Yes
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Standard parent ![](/pdbe/static/images/help.png)
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DG
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Defined at ![](/pdbe/static/images/help.png)
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2001-10-09
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Last modified at ![](/pdbe/static/images/help.png)
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2011-06-04
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Status ![](/pdbe/static/images/help.png)
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Released
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Obsoleted ![](/pdbe/static/images/help.png)
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Not Assigned
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M1G : Atoms of Molecule
Total Number of Atoms: 40
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
P |
P |
P |
N |
N |
N |
0 |
-0.733 |
0.435 |
-5.652 |
2 |
OP1 |
O |
O1P |
N |
N |
N |
0 |
-1.548 |
-0.794 |
-5.536 |
3 |
OP2 |
O |
O2P |
N |
N |
N |
0 |
-1.648 |
1.635 |
-6.212 |
4 |
OP3 |
O |
O3P |
N |
N |
Y |
0 |
0.49 |
0.174 |
-6.666 |
5 |
O5' |
O |
O5* |
N |
N |
N |
0 |
-0.153 |
0.833 |
-4.204 |
6 |
C5' |
C |
C5* |
N |
N |
N |
0 |
0.646 |
-0.265 |
-3.762 |
7 |
C4' |
C |
C4* |
R |
N |
N |
0 |
1.229 |
0.049 |
-2.384 |
8 |
O4' |
O |
O4* |
N |
N |
N |
0 |
0.169 |
0.241 |
-1.419 |
9 |
C3' |
C |
C3* |
S |
N |
N |
0 |
2.036 |
-1.152 |
-1.845 |
10 |
O3' |
O |
O3* |
N |
N |
N |
0 |
3.433 |
-0.963 |
-2.078 |
11 |
C2' |
C |
C2* |
N |
N |
N |
0 |
1.735 |
-1.162 |
-0.33 |
12 |
C1' |
C |
C1* |
R |
N |
N |
0 |
0.783 |
0.037 |
-0.128 |
13 |
N9 |
N |
N9 |
N |
Y |
N |
0 |
-0.232 |
-0.281 |
0.877 |
14 |
C8 |
C |
C8 |
N |
Y |
N |
0 |
-1.451 |
-0.848 |
0.642 |
15 |
N7 |
N |
N7 |
N |
Y |
N |
0 |
-2.097 |
-0.989 |
1.763 |
16 |
C5 |
C |
C5 |
N |
Y |
N |
0 |
-1.335 |
-0.524 |
2.783 |
17 |
C6 |
C |
C6 |
N |
N |
N |
0 |
-1.516 |
-0.426 |
4.178 |
18 |
O6 |
O |
O6 |
N |
N |
N |
0 |
-2.547 |
-0.814 |
4.701 |
19 |
N1 |
N |
N1 |
N |
N |
N |
0 |
-0.522 |
0.106 |
4.923 |
20 |
C2 |
C |
C2 |
N |
N |
N |
0 |
0.633 |
0.54 |
4.331 |
21 |
N2 |
N |
N2 |
N |
N |
N |
0 |
1.614 |
1.067 |
5.079 |
22 |
N3 |
N |
N3 |
N |
N |
N |
0 |
0.808 |
0.45 |
3.017 |
23 |
C4 |
C |
C4 |
N |
Y |
N |
0 |
-0.129 |
-0.069 |
2.228 |
24 |
C6A |
C |
C6A |
N |
N |
N |
0 |
1.49 |
1.178 |
6.381 |
25 |
C7A |
C |
C7A |
N |
N |
N |
0 |
0.32 |
0.744 |
7.019 |
26 |
C8A |
C |
C8A |
N |
N |
N |
0 |
-0.679 |
0.209 |
6.276 |
27 |
HOP2 |
H |
2HOP |
N |
N |
N |
0 |
-1.974 |
1.356 |
-7.079 |
28 |
HOP3 |
H |
3HOP |
N |
N |
N |
0 |
0.994 |
0.998 |
-6.713 |
29 |
H5' |
H |
1H5* |
N |
N |
N |
0 |
1.457 |
-0.432 |
-4.471 |
30 |
H5'' |
H |
2H5* |
N |
N |
N |
0 |
0.028 |
-1.161 |
-3.699 |
31 |
H4' |
H |
H4* |
N |
N |
N |
0 |
1.861 |
0.936 |
-2.434 |
32 |
H3' |
H |
H3* |
N |
N |
N |
0 |
1.695 |
-2.079 |
-2.308 |
33 |
HO3' |
H |
H3T |
N |
N |
Y |
0 |
3.886 |
-1.727 |
-1.695 |
34 |
H2' |
H |
1H2* |
N |
N |
N |
0 |
1.244 |
-2.092 |
-0.044 |
35 |
H2'' |
H |
2H2* |
N |
N |
N |
0 |
2.653 |
-1.022 |
0.241 |
36 |
H1' |
H |
H1* |
N |
N |
N |
0 |
1.346 |
0.922 |
0.167 |
37 |
H8 |
H |
H8 |
N |
N |
N |
0 |
-1.824 |
-1.135 |
-0.328 |
38 |
H6A |
H |
H6A |
N |
N |
N |
0 |
2.293 |
1.606 |
6.963 |
39 |
H7A |
H |
H7A |
N |
N |
N |
0 |
0.216 |
0.835 |
8.09 |
40 |
H8A |
H |
H8A |
N |
N |
N |
0 |
-1.589 |
-0.13 |
6.748 |
M1G : Chemical Bonds
Total Number of Bonds: 43
M1G : Used in PDB Entries
Total Number of PDB Entries: 3
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
M1G |
1k29 ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724397234137) |
Polymer component
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1 |
1 |
M1G |
2v4q ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724397234137) |
Polymer component
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1 |
1 |
M1G |
2v4r ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724397234137) |
Polymer component
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1 |
1 |
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