Chemical Components in the PDB

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M1G : Summary

Code

M1G

One-letter code

G

Molecule name

3-(2-DEOXY-BETA-D-RIBOFURANOSYL)-PYRIDO[5,6-A]-PURINE-10-ONE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 10.04 3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)pyrimido[1,2-a]purin-10(3H)-one
OpenEye OEToolkits 1.5.0 [(2R,3S,5R)-3-hydroxy-5-(10-oxopyrimido[1,2-a]purin-3-yl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C13 H14 N5 O7 P

Formal charge

0

Molecular weight

383.253 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C2c3ncn(c3N=C1N=CC=CN12)C4OC(C(O)C4)COP(=O)(O)O
SMILES CACTVS 3.341 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3C(=O)N4C=CC=NC4=Nc23
SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1C3CC(C(O3)COP(=O)(O)O)O)N=C4N=CC=CN4C2=O
Canonical SMILES 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 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

IUPAC InChI

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

VHESJINRMVWRRK-DJLDLDEBSA-N
M1G

wwPDB Information

Atom count

40 (26 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DG

Defined at

2001-10-09

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



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
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P OP1 P O doub 1.48 N N
2 P OP2 P O sing 1.61 N N
3 P OP3 P O sing 1.61 N N
4 P O5' P O sing 1.61 N N
5 OP2 HOP2 O H sing 0.97 N N
6 OP3 HOP3 O H sing 0.97 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C5' H5' C H sing 1.09 N N
10 C5' H5'' C H sing 1.09 N N
11 C4' O4' C O sing 1.45 N N
12 C4' C3' C C sing 1.54 N N
13 C4' H4' C H sing 1.09 N N
14 O4' C1' O C sing 1.44 N N
15 C3' O3' C O sing 1.43 N N
16 C3' C2' C C sing 1.54 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 C2' C1' C C sing 1.54 N N
20 C2' H2' C H sing 1.09 N N
21 C2' H2'' C H sing 1.09 N N
22 C1' N9 C N sing 1.46 N N
23 C1' H1' C H sing 1.09 N N
24 N9 C8 N C sing 1.36 N Y
25 N9 C4 N C sing 1.37 N Y
26 C8 N7 C N doub 1.3 N Y
27 C8 H8 C H sing 1.08 N N
28 N7 C5 N C sing 1.36 N Y
29 C5 C6 C C sing 1.41 N N
30 C5 C4 C C doub 1.4 N Y
31 C6 O6 C O doub 1.22 N N
32 C6 N1 C N sing 1.35 N N
33 N1 C2 N C sing 1.37 N N
34 N1 C8A N C sing 1.37 N N
35 C2 N2 C N sing 1.34 N N
36 C2 N3 C N doub 1.33 N N
37 N2 C6A N C doub 1.31 N N
38 N3 C4 N C sing 1.33 N N
39 C6A C7A C C sing 1.4 N N
40 C6A H6A C H sing 1.08 N N
41 C7A C8A C C doub 1.36 N N
42 C7A H7A C H sing 1.08 N N
43 C8A H8A C H sing 1.08 N N



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 Polymer component 1 1
M1G 2v4q Open in New Window Polymer component 1 1
M1G 2v4r Open in New Window Polymer component 1 1