Chemical Components in the PDB

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O2G : Summary

Code

O2G

One-letter code

G

Molecule name

2'-DEOXY-N,N-DIMETHYL-5'-O-[OXIDO(OXO)PHOSPHONIO]GUANOSINE

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-deoxy-N,N-dimethylguanosine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.6.1 [(2R,3S,5R)-5-(2-dimethylamino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C12 H18 N5 O7 P

Formal charge

0

Molecular weight

375.274 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C1c2ncn(c2N=C(N(C)C)N1)C3OC(C(O)C3)COP(=O)(O)O
SMILES CACTVS 3.352 CN(C)C1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3
SMILES OpenEye OEToolkits 1.6.1 CN(C)C1=Nc2c(ncn2C3CC(C(O3)COP(=O)(O)O)O)C(=O)N1
Canonical SMILES CACTVS 3.352 CN(C)C1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3
Canonical SMILES OpenEye OEToolkits 1.6.1 CN(C)C1=Nc2c(ncn2[C@H]3C[C@@H]([C@H](O3)COP(=O)(O)O)O)C(=O)N1

IUPAC InChI

InChI=1S/C12H18N5O7P/c1-16(2)12-14-10-9(11(19)15-12)13-5-17(10)8-3-6(18)7(24-8)4-23-25(20,21)22/h5-8,18H,3-4H2,1-2H3,(H,14,15,19)(H2,20,21,22)/t6-,7+,8+/m0/s1

IUPAC InChI key

CAVFKMBOCISJHQ-XLPZGREQSA-N
O2G

wwPDB Information

Atom count

43 (25 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

G

Defined at

2009-01-22

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



O2G : Atoms of Molecule

Total Number of Atoms: 43
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 5.512 -0.55 -0.602
2 OP1 O OP1 N N N 0 5.962 -0.85 -2.119
3 OP2 O OP2 N N N 0 6.501 0.344 0.039
4 O5' O O5' N N N 0 4.067 0.16 -0.602
5 C5' C C5' N N N 0 3.439 0.646 0.586
6 C4' C C4' R N N 0 2.083 1.26 0.231
7 O4' O O4' N N N 0 1.173 0.244 -0.242
8 C3' C C3' S N N 0 1.383 1.809 1.501
9 O3' O O3' N N N 0 1.805 3.146 1.778
10 C2' C C2' N N N 0 -0.109 1.774 1.09
11 C1' C C1' R N N 0 -0.158 0.758 -0.068
12 N9 N N9 N Y N 0 -1.074 -0.334 0.266
13 C6 C C6 N N N 0 -4.262 -1.874 0.456
14 C8 C C8 N Y N 0 -0.734 -1.529 0.832
15 N7 N N7 N Y N 0 -1.798 -2.261 0.989
16 C5 C C5 N Y N 0 -2.88 -1.583 0.536
17 O6 O O6 N N N 0 -4.7 -2.941 0.852
18 N1 N N1 N N N 0 -5.085 -0.94 -0.068
19 C2 C C2 N N N 0 -4.585 0.25 -0.507
20 N2 N N2 N N N 0 -5.445 1.18 -1.035
21 N3 N N3 N N N 0 -3.303 0.532 -0.438
22 C4 C C4 N Y N 0 -2.429 -0.342 0.074
23 CM1 C CM1 N N N 0 -4.951 2.51 -1.4
24 CM2 C CM2 N N N 0 -6.857 0.844 -1.233
25 H5' H H5' N N N 0 3.293 -0.178 1.283
26 H5'A H H5'A N N N 0 4.072 1.405 1.047
27 H4' H H4' N N N 0 2.202 2.046 -0.514
28 H3' H H3' N N N 0 1.567 1.16 2.357
29 HO3' H HO3' N N N 0 1.395 3.533 2.564
30 H2' H H2' N N N 0 -0.726 1.434 1.921
31 H2'A H H2'A N N N 0 -0.433 2.757 0.749
32 H1' H H1' N N N 0 -0.486 1.254 -0.982
33 H8 H H8 N N N 0 0.268 -1.822 1.107
34 HN1 H HN1 N N N 0 -6.037 -1.117 -0.134
35 HM1 H HM1 N N N 0 -4.615 2.5 -2.437
36 HM1A H HM1A N N N 0 -5.753 3.24 -1.285
37 HM1B H HM1B N N N 0 -4.118 2.78 -0.751
38 HM2 H HM2 N N N 0 -7.055 -0.147 -0.824
39 HM2A H HM2A N N N 0 -7.481 1.578 -0.724
40 HM2B H HM2B N N N 0 -7.086 0.849 -2.299
41 OP3 O OP3 N N Y 0 5.429 -1.934 0.216
42 HP3 H HP3 N N N 0 4.799 -2.57 -0.149
43 HP1 H HP1 N N N 0 6.826 -1.278 -2.195



O2G : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P OP3 P O sing 1.61 N N
2 OP3 HP3 O H sing 0.97 N N
3 OP1 HP1 O H sing 0.97 N N
4 P OP1 P O sing 1.61 N N
5 P OP2 P O doub 1.48 N N
6 P O5' P O sing 1.61 N N
7 O5' C5' O C sing 1.43 N N
8 C5' C4' C C sing 1.53 N N
9 C4' O4' C O sing 1.44 N N
10 C4' C3' C C sing 1.55 N N
11 C3' O3' C O sing 1.43 N N
12 C3' C2' C C sing 1.55 N N
13 O4' C1' O C sing 1.44 N N
14 C2' C1' C C sing 1.54 N N
15 C1' N9 C N sing 1.46 N N
16 N9 C8 N C sing 1.37 N Y
17 C8 N7 C N doub 1.3 N Y
18 N7 C5 N C sing 1.35 N Y
19 C5 C6 C C sing 1.41 N N
20 C6 O6 C O doub 1.22 N N
21 C6 N1 C N sing 1.35 N N
22 N1 C2 N C sing 1.36 N N
23 C2 N2 C N sing 1.37 N N
24 C2 N3 C N doub 1.31 N N
25 N9 C4 N C sing 1.37 N Y
26 C5 C4 C C doub 1.4 N Y
27 N3 C4 N C sing 1.34 N N
28 N2 CM1 N C sing 1.46 N N
29 N2 CM2 N C sing 1.46 N N
30 C5' H5' C H sing 1.09 N N
31 C5' H5'A C H sing 1.09 N N
32 C4' H4' C H sing 1.09 N N
33 C3' H3' C H sing 1.09 N N
34 O3' HO3' O H sing 0.97 N N
35 C2' H2' C H sing 1.09 N N
36 C2' H2'A C H sing 1.09 N N
37 C1' H1' C H sing 1.09 N N
38 C8 H8 C H sing 1.08 N N
39 N1 HN1 N H sing 0.97 N N
40 CM1 HM1 C H sing 1.09 N N
41 CM1 HM1A C H sing 1.09 N N
42 CM1 HM1B C H sing 1.09 N N
43 CM2 HM2 C H sing 1.09 N N
44 CM2 HM2A C H sing 1.09 N N
45 CM2 HM2B C H sing 1.09 N N



O2G : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
O2G 2w9a Open in New Window Polymer component 1 1
O2G 2w9b Open in New Window Polymer component 2 1
O2G 2w9c Open in New Window Polymer component 2 1