Chemical Components in the PDB

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18M : Summary

Code

18M

One-letter code

G

Molecule name

2'-O-methylguanosine 3',5'-bis(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 2'-O-methylguanosine 3',5'-bis(dihydrogen phosphate)
OpenEye OEToolkits 1.7.6 [(2R,3R,4R,5R)-5-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-4-methoxy-2-(phosphonooxymethyl)oxolan-3-yl] dihydrogen phosphate

Formula

C11 H17 N5 O11 P2

Formal charge

0

Molecular weight

457.227 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC3OC(n1cnc2c1NC(=NC2=O)N)C(OC)C3OP(=O)(O)O
SMILES CACTVS 3.370 CO[CH]1[CH](O[P](O)(O)=O)[CH](CO[P](O)(O)=O)O[CH]1n2cnc3C(=O)N=C(N)Nc23
SMILES OpenEye OEToolkits 1.7.6 COC1C(C(OC1n2cnc3c2NC(=NC3=O)N)COP(=O)(O)O)OP(=O)(O)O
Canonical SMILES CACTVS 3.370 CO[C@@H]1[C@H](O[P](O)(O)=O)[C@@H](CO[P](O)(O)=O)O[C@H]1n2cnc3C(=O)N=C(N)Nc23
Canonical SMILES OpenEye OEToolkits 1.7.6 CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2NC(=NC3=O)N)COP(=O)(O)O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C11H17N5O11P2/c1-24-7-6(27-29(21,22)23)4(2-25-28(18,19)20)26-10(7)16-3-13-5-8(16)14-11(12)15-9(5)17/h3-4,6-7,10H,2H2,1H3,(H2,18,19,20)(H2,21,22,23)(H3,12,14,15,17)/t4-,6-,7-,10-/m1/s1

IUPAC InChI key

SKZHCLKZMCYMDN-KQYNXXCUSA-N
18M

wwPDB Information

Atom count

46 (29 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

G

Defined at

2012-11-07

Last modified at

2012-11-16

Status

Released

Obsoleted

Not Assigned



18M : Atoms of Molecule

Total Number of Atoms: 46
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1' R N N 0 -0.944 0.277 0.706
2 C2 C C2 N N N 0 -5.476 0.082 0.934
3 C2' C C2' R N N 0 -0.637 -1.172 0.266
4 C3' C C3' R N N 0 0.863 -1.142 -0.116
5 C4 C C4 N Y N 0 -3.351 0.681 0.071
6 C4' C C4' R N N 0 1.365 0.116 0.638
7 C5 C C5 N Y N 0 -3.981 1.378 -0.952
8 C5' C C5' N N N 0 2.613 0.687 -0.038
9 C6 C C6 N N N 0 -5.447 1.385 -0.983
10 C8 C C8 N Y N 0 -1.848 1.597 -1.246
11 CM2 C CM2 N N N 0 -2.153 -2.687 1.339
12 H1' H H1' N N N 0 -1.243 0.29 1.754
13 H2' H H2' N N N 0 -1.245 -1.447 -0.596
14 H3' H H3' N N N 0 0.988 -1.026 -1.192
15 H4' H H4' N N N 0 1.569 -0.119 1.683
16 H5' H H5' N N N 0 2.364 1.009 -1.048
17 H5'A H H5'A N N N 0 3.386 -0.081 -0.081
18 H8 H H8 N N N 0 -0.897 1.891 -1.665
19 HM2 H HM2 N N N 0 -2.243 -3.361 2.19
20 HM2A H HM2A N N N 0 -2.919 -1.914 1.405
21 HM2B H HM2B N N N 0 -2.284 -3.25 0.414
22 HN2 H HN2 N N N 0 -7.177 -0.556 1.851
23 HN2A H HN2A N N N 0 -5.758 -1.053 2.6
24 HN3 H HN3 N N N 0 -3.693 -0.445 1.731
25 HO11 H HO11 N N N 0 0.712 -4.502 -1.308
26 HO13 H HO13 N N N 0 3.639 -5.038 -0.254
27 HOP1 H HOP1 N N N 0 5.49 4.292 1.239
28 HOP3 H HOP3 N N N 0 3.375 4.011 -1.087
29 N1 N N1 N N N 0 -6.112 0.726 -0.021
30 N2 N N2 N N N 0 -6.208 -0.572 1.887
31 N3 N N3 N N N 0 -4.12 0.042 1.009
32 N7 N N7 N Y N 0 -3.014 1.916 -1.731
33 N9 N N9 N Y N 0 -2.013 0.834 -0.127
34 O11 O O11 N N N 0 1.413 -3.962 -1.697
35 O12 O O12 N N N 0 3.42 -2.479 -1.317
36 O13 O O13 N N N 0 3.103 -4.421 0.264
37 O2' O O2' N N N 0 -0.86 -2.079 1.347
38 O3' O O3' N N N 0 1.531 -2.316 0.35
39 O4' O O4' N N N 0 0.261 1.04 0.531
40 O5' O O5' N N N 0 3.093 1.804 0.714
41 O6 O O6 N N N 0 -6.049 1.979 -1.863
42 OP1 O OP1 N N N 0 4.716 3.745 1.428
43 OP2 O OP2 N N N 0 5.551 1.737 0.145
44 OP3 O OP3 N N N 0 4.12 3.396 -1.109
45 P P P N N N 0 4.395 2.65 0.291
46 P1 P P1 N N N 0 2.389 -3.277 -0.616



18M : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP2 P O P doub 1.4802773 N N
2 O5' P O P sing 1.6093007 N N
3 P OP3 P O sing 1.6100128 N N
4 P OP1 P O sing 1.6108491 N N
5 O5' C5' O C sing 1.4295429 N N
6 C4' C5' C C sing 1.5298761 N N
7 C5' H5' C H sing 1.0889375 N N
8 C5' H5'A C H sing 1.0905054 N N
9 C3' C4' C C sing 1.5501884 N N
10 O4' C4' O C sing 1.4436208 N N
11 C4' H4' C H sing 1.0903513 N N
12 C1' O4' C O sing 1.4369478 N N
13 C2' C3' C C sing 1.548168 N N
14 C3' O3' C O sing 1.4288653 N N
15 C3' H3' C H sing 1.0894296 N N
16 O3' P1 O P sing 1.6102301 N N
17 O2' C2' O C sing 1.4286144 N N
18 C2' C1' C C sing 1.5451375 N N
19 C2' H2' C H sing 1.0901068 N N
20 O2' CM2 O C sing 1.4288377 N N
21 N9 C1' N C sing 1.46523 N N
22 C1' H1' C H sing 1.0898963 N N
23 C8 N9 C N sing 1.3643881 N Y
24 C4 N9 C N sing 1.3611969 N Y
25 N7 C8 N C doub 1.3025137 N Y
26 C8 H8 C H sing 1.0799991 N N
27 N7 C5 N C sing 1.3532827 N Y
28 C6 C5 C C sing 1.4663445 N N
29 C5 C4 C C doub 1.3889701 N Y
30 O6 C6 O C doub 1.2205081 N N
31 C6 N1 C N sing 1.3423673 N N
32 N1 C2 N C doub 1.3157724 N N
33 C2 N3 C N sing 1.3586615 N N
34 C2 N2 C N sing 1.3681188 N N
35 N2 HN2 N H sing 0.9698005 N N
36 N2 HN2A N H sing 0.9706853 N N
37 C4 N3 C N sing 1.3709581 N N
38 N3 HN3 N H sing 0.9699392 N N
39 O12 P1 O P doub 1.4802587 N N
40 P1 O13 P O sing 1.6102583 N N
41 P1 O11 P O sing 1.6094601 N N
42 O11 HO11 O H sing 0.96660334 N N
43 O13 HO13 O H sing 0.9676306 N N
44 CM2 HM2 C H sing 1.0893011 N N
45 CM2 HM2A C H sing 1.0902481 N N
46 CM2 HM2B C H sing 1.0907589 N N
47 OP1 HOP1 O H sing 0.96643984 N N
48 OP3 HOP3 O H sing 0.9662991 N N



18M : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
18M 4hqu Open in New Window Polymer component 1 1
18M 4hqx Open in New Window Polymer component 1 1