Chemical Components in the PDB

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G5J : Summary

Code

G5J

One-letter code

X

Molecule name

5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine

Systematic names

ProgramVersionName
ACDLabs 12.01 5'-O-[(S)-hydroxy{[(R)-hydroxy{[(S)-hydroxy(methoxy)phosphoryl]oxy}phosphoryl]oxy}phosphoryl]guanosine
OpenEye OEToolkits 2.0.6 [[(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [methoxy(oxidanyl)phosphoryl] hydrogen phosphate

Formula

C11 H18 N5 O14 P3

Formal charge

0

Molecular weight

537.207 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C3(=NC(c2c(n(C1OC(C(O)C1O)COP(O)(=O)OP(O)(=O)OP(=O)(O)OC)cn2)N3)=O)N
SMILES CACTVS 3.385 CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3C(=O)N=C(N)Nc23
SMILES OpenEye OEToolkits 2.0.6 COP(=O)(O)OP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2NC(=NC3=O)N)O)O
Canonical SMILES CACTVS 3.385 CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3C(=O)N=C(N)Nc23
Canonical SMILES OpenEye OEToolkits 2.0.6 COP(=O)(O)OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2NC(=NC3=O)N)O)O

IUPAC InChI

InChI=1S/C11H18N5O14P3/c1-26-31(20,21)29-33(24,25)30-32(22,23)27-2-4-6(17)7(18)10(28-4)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)(H,22,23)(H,24,25)(H3,12,14,15,19)/t4-,6-,7-,10-/m1/s1

IUPAC InChI key

DJZJYVFASQUZKQ-KQYNXXCUSA-N
G5J

wwPDB Information

Atom count

51 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-05-07

Last modified at

2018-12-14

Status

Released

Obsoleted

Not Assigned



G5J : Atoms of Molecule

Total Number of Atoms: 51
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 N N N 0 -6.981 -1.89 -1.105
2 N2 N N1 N N N 0 -7.828 -1.849 -2.18
3 C4 C C2 N Y N 0 -5.071 -1.025 0.001
4 C5 C C3 N Y N 0 -5.264 -1.95 1.02
5 C6 C C4 N N N 0 -6.399 -2.871 0.912
6 O6 O O1 N N N 0 -6.612 -3.703 1.781
7 O2' O O2 N N N 0 -5.039 2.495 -0.996
8 O3' O O3 N N N 0 -3.114 4.16 -1.073
9 O4' O O4 N N N 0 -1.982 0.949 -0.097
10 O5' O O5 N N N 0 0.735 1.994 -0.19
11 C1' C C5 R N N 0 -3.378 0.792 -0.433
12 C2' C C6 R N N 0 -4.031 2.138 -0.048
13 C3' C C7 S N N 0 -2.862 3.148 -0.095
14 C3G C C8 N N N 0 7.007 -4.041 -1.776
15 C4' C C9 R N N 0 -1.642 2.293 -0.503
16 C5' C C10 N N N 0 -0.388 2.77 0.232
17 C8 C C11 N Y N 0 -3.513 -0.785 1.533
18 N1 N N2 N N N 0 -7.199 -2.781 -0.162
19 N3 N N3 N N N 0 -5.945 -1.012 -1.055
20 N7 N N4 N Y N 0 -4.281 -1.758 1.931
21 N9 N N5 N Y N 0 -3.968 -0.303 0.341
22 O1A O O6 N N N 0 2.749 3.68 -0.064
23 O1B O O7 N N N 0 5.789 1.576 -0.133
24 O1G O O8 N N N 0 7.212 -1.626 0.197
25 O2A O O9 N N N 0 2.205 2.135 1.857
26 O2B O O10 N N N 0 4.637 0.266 1.692
27 O2G O O11 N N N 0 5.254 -3.089 0.828
28 O3A O O12 N N N 0 3.206 1.095 -0.214
29 O3B O O13 N N N 0 4.92 -0.871 -0.544
30 O3G O O14 N N N 0 6.107 -2.937 -1.655
31 PA P P1 N N N 0 2.224 2.224 0.38
32 PB P P2 N N N 0 4.638 0.511 0.232
33 PG P P3 N N N 0 5.902 -2.12 -0.283
34 H1 H H1 N N N 0 -8.571 -2.47 -2.236
35 H2 H H2 N N N 0 -7.684 -1.199 -2.886
36 H3 H H3 N N N 0 -5.482 3.332 -0.803
37 H4 H H4 N N N 0 -3.905 4.688 -0.898
38 H5 H H5 N N N 0 -3.493 0.606 -1.501
39 H6 H H6 N N N 0 -4.452 2.085 0.955
40 H7 H H7 N N N 0 -2.706 3.597 0.886
41 H8 H H8 N N N 0 8.02 -3.71 -1.549
42 H9 H H9 N N N 0 6.715 -4.826 -1.078
43 H10 H H10 N N N 0 6.971 -4.428 -2.795
44 H11 H H11 N N N 0 -1.491 2.337 -1.581
45 H12 H H12 N N N 0 -0.529 2.65 1.306
46 H13 H H13 N N N 0 -0.211 3.821 0.004
47 H14 H H14 N N N 0 -2.648 -0.416 2.064
48 H15 H H15 N N N 0 -5.823 -0.371 -1.773
49 H16 H H16 N N N 0 2.787 3.81 -1.021
50 H17 H H17 N N N 0 5.847 1.785 -1.075
51 H18 H H18 N N N 0 4.392 -3.451 0.58



G5J : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N2 C2 N C sing 1.37 N N
2 C2 N1 C N doub 1.32 N N
3 C2 N3 C N sing 1.36 N N
4 N1 C6 N C sing 1.34 N N
5 N3 C4 N C sing 1.37 N N
6 C6 O6 C O doub 1.22 N N
7 C6 C5 C C sing 1.47 N N
8 C4 C5 C C doub 1.39 N Y
9 C4 N9 C N sing 1.36 N Y
10 O2' C2' O C sing 1.43 N N
11 C5 N7 C N sing 1.35 N Y
12 C2' C1' C C sing 1.54 N N
13 C2' C3' C C sing 1.55 N N
14 N9 C1' N C sing 1.46 N N
15 N9 C8 N C sing 1.36 N Y
16 C1' O4' C O sing 1.44 N N
17 N7 C8 N C doub 1.3 N Y
18 O3' C3' O C sing 1.43 N N
19 C3' C4' C C sing 1.54 N N
20 O4' C4' O C sing 1.44 N N
21 C4' C5' C C sing 1.53 N N
22 O5' C5' O C sing 1.43 N N
23 O5' PA O P sing 1.61 N N
24 O2B PB O P doub 1.48 N N
25 O2A PA O P doub 1.48 N N
26 PA O1A P O sing 1.61 N N
27 PA O3A P O sing 1.61 N N
28 PB O3A P O sing 1.61 N N
29 PB O1B P O sing 1.61 N N
30 PB O3B P O sing 1.61 N N
31 O3B PG O P sing 1.61 N N
32 PG O1G P O doub 1.48 N N
33 PG O2G P O sing 1.61 N N
34 PG O3G P O sing 1.61 N N
35 O3G C3G O C sing 1.43 N N
36 N2 H1 N H sing 0.97 N N
37 N2 H2 N H sing 0.97 N N
38 O2' H3 O H sing 0.97 N N
39 O3' H4 O H sing 0.97 N N
40 C1' H5 C H sing 1.09 N N
41 C2' H6 C H sing 1.09 N N
42 C3' H7 C H sing 1.09 N N
43 C3G H8 C H sing 1.09 N N
44 C3G H9 C H sing 1.09 N N
45 C3G H10 C H sing 1.09 N N
46 C4' H11 C H sing 1.09 N N
47 C5' H12 C H sing 1.09 N N
48 C5' H13 C H sing 1.09 N N
49 C8 H14 C H sing 1.08 N N
50 N3 H15 N H sing 0.97 N N
51 O1A H16 O H sing 0.97 N N
52 O1B H17 O H sing 0.97 N N
53 O2G H18 O H sing 0.97 N N



G5J : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
G5J 6dcc Open in New Window Polymer component 1 1
G5J 7dvq Open in New Window Bound ligand 1 1
G5J 7slp Open in New Window Polymer component 1 1
G5J 7slq Open in New Window Polymer component 1 1