Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

CG1 : Summary

Code

CG1

One-letter code

G

Molecule name

5'-O-[(R)-hydroxy(methoxy)phosphoryl]guanosine

Systematic names

ProgramVersionName
ACDLabs 10.04 5'-O-[(R)-hydroxy(methoxy)phosphoryl]guanosine
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl methyl hydrogen phosphate

Formula

C11 H16 N5 O8 P

Formal charge

0

Molecular weight

377.247 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(OC)OCC3OC(n2cnc1c2N=C(N)NC1=O)C(O)C3O
SMILES CACTVS 3.341 CO[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=O)NC(=Nc23)N
SMILES OpenEye OEToolkits 1.5.0 COP(=O)(O)OCC1C(C(C(O1)n2cnc3c2N=C(NC3=O)N)O)O
Canonical SMILES CACTVS 3.341 CO[P@](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)NC(=Nc23)N
Canonical SMILES OpenEye OEToolkits 1.5.0 CO[P@@](=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2N=C(NC3=O)N)O)O

IUPAC InChI

InChI=1S/C11H16N5O8P/c1-22-25(20,21)23-2-4-6(17)7(18)10(24-4)16-3-13-5-8(16)14-11(12)15-9(5)19/h3-4,6-7,10,17-18H,2H2,1H3,(H,20,21)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1

IUPAC InChI key

CTLHMSXPFVHJEK-KQYNXXCUSA-N
CG1

wwPDB Information

Atom count

41 (25 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

G

Defined at

2008-03-26

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



CG1 : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 OP3 O OP3 N N N 0 -5.354 1.555 -1.112
2 P P P R N N 0 -4.864 0.526 0.026
3 OP1 O OP1 N N N 0 -5.959 -0.641 0.201
4 OP2 O OP2 N N N 0 -4.703 1.248 1.308
5 O5' O O5' N N N 0 -3.455 -0.121 -0.406
6 C5' C C5' N N N 0 -2.708 -0.996 0.441
7 C4' C C4' R N N 0 -1.425 -1.426 -0.273
8 O4' O O4' N N N 0 -0.56 -0.292 -0.449
9 C3' C C3' S N N 0 -0.665 -2.453 0.588
10 O3' O O3' N N N 0 -0.524 -3.689 -0.116
11 C2' C C2' R N N 0 0.719 -1.8 0.824
12 O2' O O2' N N N 0 1.765 -2.768 0.72
13 C1' C C1' R N N 0 0.796 -0.774 -0.336
14 N9 N N9 N Y N 0 1.707 0.321 0.005
15 C8 C C8 N Y N 0 1.356 1.524 0.546
16 N7 N N7 N Y N 0 2.417 2.257 0.718
17 C5 C C5 N Y N 0 3.509 1.571 0.299
18 C6 C C6 N N N 0 4.893 1.858 0.248
19 O6 O O6 N N N 0 5.323 2.93 0.638
20 N1 N N1 N N N 0 5.726 0.915 -0.245
21 C2 C C2 N N N 0 5.234 -0.28 -0.678
22 N2 N N2 N N N 0 6.104 -1.219 -1.173
23 N3 N N3 N N N 0 3.95 -0.559 -0.636
24 C4 C C4 N Y N 0 3.066 0.324 -0.156
25 H5' H H5' N N N 0 -2.452 -0.476 1.365
26 H5'A H H5'A N N N 0 -3.307 -1.876 0.674
27 H4' H H4' N N N 0 -1.669 -1.86 -1.243
28 H3' H H3' N N N 0 -1.179 -2.612 1.536
29 H2' H H2' N N N 0 0.751 -1.297 1.791
30 C C C N N N 0 -6.52 2.369 -0.975
31 H1' H H1' N N N 0 1.109 -1.262 -1.259
32 HOP1 H HOP1 N N N 0 -6.116 -1.156 -0.602
33 HO3' H HO3' N N N 0 -0.052 -4.372 0.38
34 HO2' H HO2' N N N 0 1.706 -3.482 1.369
35 H8 H H8 N N N 0 0.348 1.823 0.794
36 HN1 H HN1 N N N 0 6.679 1.09 -0.29
37 HN2 H HN2 N N N 0 7.054 -1.027 -1.211
38 HN2A H HN2A N N N 0 5.768 -2.073 -1.485
39 H H H N N N 0 -7.395 1.732 -0.845
40 HA H HA N N N 0 -6.411 3.018 -0.106
41 HB H HB N N N 0 -6.644 2.979 -1.87



CG1 : 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 OP3 P O sing 1.61 N N
2 OP3 C O C sing 1.43 N N
3 O5' P O P sing 1.61 N N
4 OP2 P O P doub 1.48 N N
5 P OP1 P O sing 1.61 N N
6 OP1 HOP1 O H sing 0.97 N N
7 C5' O5' C O sing 1.43 N N
8 C4' C5' C C sing 1.53 N N
9 H5'A C5' H C sing 1.09 N N
10 C5' H5' C H sing 1.09 N N
11 C3' C4' C C sing 1.54 N N
12 H4' C4' H C sing 1.09 N N
13 C4' O4' C O sing 1.44 N N
14 C1' O4' C O sing 1.44 N N
15 O3' C3' O C sing 1.43 N N
16 C2' C3' C C sing 1.55 N N
17 C3' H3' C H sing 1.09 N N
18 O3' HO3' O H sing 0.97 N N
19 O2' C2' O C sing 1.43 N N
20 H2' C2' H C sing 1.09 N N
21 C2' C1' C C sing 1.55 N N
22 O2' HO2' O H sing 0.97 N N
23 C1' N9 C N sing 1.46 N N
24 C1' H1' C H sing 1.09 N N
25 C4 N9 C N sing 1.37 N Y
26 N9 C8 N C sing 1.36 N Y
27 C8 N7 C N doub 1.3 N Y
28 C8 H8 C H sing 1.08 N N
29 C5 N7 C N sing 1.36 N Y
30 C4 C5 C C doub 1.4 N Y
31 C5 C6 C C sing 1.41 N N
32 N1 C6 N C sing 1.35 N N
33 C6 O6 C O doub 1.22 N N
34 C2 N1 C N sing 1.36 N N
35 N1 HN1 N H sing 0.97 N N
36 N2 C2 N C sing 1.37 N N
37 N3 C2 N C doub 1.31 N N
38 N2 HN2 N H sing 0.97 N N
39 N2 HN2A N H sing 0.97 N N
40 N3 C4 N C sing 1.34 N N
41 C H C H sing 1.09 N N
42 C HA C H sing 1.09 N N
43 C HB C H sing 1.09 N N



CG1 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
CG1 1f6u Open in New Window Polymer component 1 1