Chemical Components in the PDB

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B9B : Summary

Code

B9B

One-letter code

G

Molecule name

6-propyl, guanosine-5'-monophosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 [(2~{R},3~{S},4~{R},5~{R})-5-(2-azanyl-6-propoxy-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl dihydrogen phosphate

Formula

C13 H20 N5 O8 P

Formal charge

0

Molecular weight

405.3 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCCOc1nc(N)nc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 2.0.6 CCCOc1c2c(nc(n1)N)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O
Canonical SMILES CACTVS 3.385 CCCOc1nc(N)nc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 2.0.6 CCCOc1c2c(nc(n1)N)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O

IUPAC InChI

InChI=1S/C13H20N5O8P/c1-2-3-24-11-7-10(16-13(14)17-11)18(5-15-7)12-9(20)8(19)6(26-12)4-25-27(21,22)23/h5-6,8-9,12,19-20H,2-4H2,1H3,(H2,14,16,17)(H2,21,22,23)/t6-,8-,9-,12-/m1/s1

IUPAC InChI key

BEBGGMIXLKQJTH-WOUKDFQISA-N
B9B

wwPDB Information

Atom count

47 (27 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

G

Defined at

2017-09-25

Last modified at

2019-04-29

Status

Released

Obsoleted

Not Assigned



B9B : Atoms of Molecule

Total Number of Atoms: 47
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 N Y N 0 -3.887 1.571 -1.083
2 C5 C C2 N Y N 0 -2.796 -0.539 0.173
3 C2' C C6 R N N 0 0.721 2.016 0.963
4 C6 C C3 N Y N 0 -4.18 -0.476 -0.05
5 C8 C C4 N Y N 0 -0.743 -1.002 0.698
6 C1' C C5 R N N 0 0.483 1.018 -0.192
7 C3' C C7 S N N 0 2.258 2.061 1.109
8 C4 C C8 N Y N 0 -1.999 0.528 -0.276
9 C4' C C9 R N N 0 2.767 1.084 0.026
10 C5' C C10 N N N 0 3.985 0.31 0.536
11 N1 N N1 N Y N 0 -4.675 0.585 -0.675
12 N2 N N2 N N N 0 -4.454 2.659 -1.725
13 N3 N N3 N Y N 0 -2.577 1.553 -0.893
14 N7 N N4 N Y N 0 -1.967 -1.438 0.758
15 N9 N N5 N Y N 0 -0.71 0.208 0.069
16 O2' O O1 N N N 0 0.213 3.307 0.621
17 O3' O O2 N N N 0 2.747 3.381 0.863
18 O4' O O3 N N N 0 1.662 0.184 -0.208
19 O6 O O5 N N N 0 -4.994 -1.477 0.362
20 O5' O O4 N N N 0 4.51 -0.5 -0.518
21 OP1 O O6 N N N 0 6.936 -0.647 0.162
22 OP2 O O7 N N N 0 5.458 -2.614 0.725
23 P P P1 N N N 0 5.797 -1.45 -0.335
24 C61 C C11 N N N 0 -6.39 -1.332 0.093
25 C62 C C12 N N N 0 -7.142 -2.552 0.628
26 C63 C C13 N N N 0 -8.637 -2.396 0.341
27 H1 H H1 N N N 0 0.12 -1.521 1.089
28 H2 H H2 N N N 0 0.381 1.549 -1.138
29 H3 H H3 N N N 0 0.26 1.654 1.882
30 H4 H H4 N N N 0 2.557 1.721 2.101
31 H5 H H5 N N N 0 3.017 1.626 -0.886
32 H6 H H6 N N N 0 4.749 1.014 0.868
33 H7 H H7 N N N 0 3.688 -0.325 1.37
34 H11 H H11 N N N 0 2.41 4.046 1.478
35 H8 H H8 N N N 0 -5.413 2.692 -1.869
36 H9 H H9 N N N 0 -3.893 3.389 -2.03
37 H10 H H10 N N N 0 0.336 3.973 1.311
38 H13 H H13 N N N 0 4.719 -3.181 0.464
39 H14 H H14 N N N 0 -6.762 -0.432 0.583
40 H15 H H15 N N N 0 -6.546 -1.251 -0.983
41 H16 H H16 N N N 0 -6.77 -3.452 0.139
42 H17 H H17 N N N 0 -6.986 -2.632 1.704
43 H18 H H18 N N N 0 -9.009 -1.496 0.83
44 H19 H H19 N N N 0 -8.793 -2.315 -0.735
45 H20 H H20 N N N 0 -9.173 -3.265 0.722
46 OP3 O OP3 N N N 0 6.182 -2.11 -1.752
47 H12 H H12 N N N 0 6.95 -2.697 -1.717



B9B : Chemical Bonds

Total Number of Bonds: 49
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2' C2' O C sing 1.43 N N
2 C61 C62 C C sing 1.53 N N
3 C61 O6 C O sing 1.43 N N
4 N2 C2 N C sing 1.38 N N
5 C2 N1 C N doub 1.33 N Y
6 C2 N3 C N sing 1.32 N Y
7 N1 C6 N C sing 1.33 N Y
8 C62 C63 C C sing 1.53 N N
9 N3 C4 N C doub 1.33 N Y
10 C6 O6 C O sing 1.35 N N
11 C6 C5 C C doub 1.4 N Y
12 C2' C1' C C sing 1.54 N N
13 C2' C3' C C sing 1.54 N N
14 O3' C3' O C sing 1.43 N N
15 C4 C5 C C sing 1.41 N Y
16 C4 N9 C N sing 1.37 N Y
17 C5 N7 C N sing 1.36 N Y
18 N9 C1' N C sing 1.47 N N
19 N9 C8 N C sing 1.36 N Y
20 C1' O4' C O sing 1.44 N N
21 N7 C8 N C doub 1.3 N Y
22 C3' C4' C C sing 1.54 N N
23 O4' C4' O C sing 1.44 N N
24 C4' C5' C C sing 1.53 N N
25 O5' C5' O C sing 1.43 N N
26 O5' P O P sing 1.61 N N
27 OP1 P O P doub 1.48 N N
28 P OP2 P O sing 1.61 N N
29 C8 H1 C H sing 1.08 N N
30 C1' H2 C H sing 1.09 N N
31 C2' H3 C H sing 1.09 N N
32 C3' H4 C H sing 1.09 N N
33 C4' H5 C H sing 1.09 N N
34 C5' H6 C H sing 1.09 N N
35 C5' H7 C H sing 1.09 N N
36 N2 H8 N H sing 0.97 N N
37 N2 H9 N H sing 0.97 N N
38 O2' H10 O H sing 0.97 N N
39 O3' H11 O H sing 0.97 N N
40 OP2 H13 O H sing 0.97 N N
41 C61 H14 C H sing 1.09 N N
42 C61 H15 C H sing 1.09 N N
43 C62 H16 C H sing 1.09 N N
44 C62 H17 C H sing 1.09 N N
45 C63 H18 C H sing 1.09 N N
46 C63 H19 C H sing 1.09 N N
47 C63 H20 C H sing 1.09 N N
48 P OP3 P O sing 1.61 N N
49 OP3 H12 O H sing 0.97 N N



B9B : Used in PDB Entries

Total Number of PDB Entries: 25
Ligand Code PDB Entry ID Type Total Distinct
B9B 6lqm Open in New Window Polymer component 3 3
B9B 6lsr Open in New Window Polymer component 3 3
B9B 6lss Open in New Window Polymer component 3 3
B9B 6lu8 Open in New Window Polymer component 3 3
B9B 6mtb Open in New Window Polymer component 3 3
B9B 6mtc Open in New Window Polymer component 3 3
B9B 6mtd Open in New Window Polymer component 3 3
B9B 6mte Open in New Window Polymer component 3 3
B9B 7ls1 Open in New Window Polymer component 3 3
B9B 7ls2 Open in New Window Polymer component 2 2
B9B 7oyd Open in New Window Polymer component 3 3
B9B 7ucj Open in New Window Polymer component 3 3
B9B 7uck Open in New Window Polymer component 3 3
B9B 8idt Open in New Window Polymer component 3 3
B9B 8idy Open in New Window Polymer component 3 3
B9B 8ie3 Open in New Window Polymer component 2 2
B9B 8ine Open in New Window Polymer component 3 3
B9B 8inf Open in New Window Polymer component 3 3
B9B 8ink Open in New Window Polymer component 3 3
B9B 8ipd Open in New Window Polymer component 3 3
B9B 8ipx Open in New Window Polymer component 3 3
B9B 8ipy Open in New Window Polymer component 3 3
B9B 8ir1 Open in New Window Polymer component 3 3
B9B 8ir3 Open in New Window Polymer component 3 3
B9B 8scb Open in New Window Polymer component 1 1