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DJF : Summary
Code
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DJF
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One-letter code
|
X
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Molecule name
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[(1S,5R,6R,8R)-6-(6-aminopurin-9-yl)-2'-(3-oxidanylpropoxy)spiro[2,4,7-trioxa-3-boranuidabicyclo[3.3.0]octane-3,9'-8-oxa-9-boranuidabicyclo[4.3.0]nona-1(6),2,4-triene]-8-yl]methyl dihydrogen phosphate
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Systematic names
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|
Formula
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C20 H24 B N5 O10 P
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Formal charge
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-1
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Molecular weight
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536.217 Da
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SMILES
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Type | Program | Version | Descriptor |
SMILES
|
CACTVS |
3.370 |
Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH]4O[B-]5(OCc6cccc(OCCCO)c56)O[CH]34 |
SMILES
|
OpenEye OEToolkits |
1.7.6 |
[B-]12(c3c(cccc3OCCCO)CO1)OC4C(OC(C4O2)n5cnc6c5ncnc6N)COP(=O)(O)O |
Canonical SMILES
|
CACTVS |
3.370 |
Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@H]4O[B-]5(OCc6cccc(OCCCO)c56)O[C@@H]34 |
Canonical SMILES
|
OpenEye OEToolkits |
1.7.6 |
[B-]12(c3c(cccc3OCCCO)CO1)O[C@@H]4[C@H](O[C@H]([C@@H]4O2)n5cnc6c5ncnc6N)COP(=O)(O)O |
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IUPAC InChI | InChI=1S/C20H22BN5O9P/c22-18-15-19(24-9-23-18)26(10-25-15)20-17-16(13(33-20)8-32-36(28)29)34-21(35-17)14-11(7-31-21)3-1-4-12(14)30-6-2-5-27/h1,3-4,9-10,13,16-17,20,27H,2,5-8H2,(H2,22,23,24)/q-1/t13-,16-,17-,20-,21+/m1/s1 |
IUPAC InChI key | QAJGLUMMRUEBOV-PGBNIQHZSA-N |
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wwPDB Information |
Atom count
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61 (37 without Hydrogen)
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Polymer type
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Ribonucleotide
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Type description
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RNA LINKING
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Type code
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ATOMN
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Is modified
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No
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Standard parent
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Not Assigned
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Defined at
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2013-01-21
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Last modified at
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2013-04-12
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Status
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Released
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Obsoleted
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Not Assigned
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DJF : Atoms of Molecule
Total Number of Atoms: 61
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
B |
B |
B |
N |
N |
N |
-1 |
0.974 |
1.593 |
-1.751 |
2 |
P |
P |
P |
N |
N |
N |
0 |
-5.732 |
0.698 |
0.671 |
3 |
N1 |
N |
N1 |
N |
Y |
N |
0 |
3.304 |
-4.978 |
0.01 |
4 |
O1 |
O |
O1 |
N |
N |
N |
0 |
1.095 |
1.616 |
-3.116 |
5 |
C2 |
C |
C2 |
N |
Y |
N |
0 |
3.457 |
-3.688 |
0.249 |
6 |
N3 |
N |
N3 |
N |
Y |
N |
0 |
2.461 |
-2.831 |
0.166 |
7 |
C4 |
C |
C4 |
N |
Y |
N |
0 |
1.241 |
-3.24 |
-0.168 |
8 |
C5 |
C |
C5 |
N |
Y |
N |
0 |
1.026 |
-4.603 |
-0.432 |
9 |
C6 |
C |
C6 |
N |
Y |
N |
0 |
2.121 |
-5.479 |
-0.33 |
10 |
N6 |
N |
N6 |
N |
N |
N |
0 |
1.97 |
-6.832 |
-0.579 |
11 |
N7 |
N |
N7 |
N |
Y |
N |
0 |
-0.284 |
-4.748 |
-0.742 |
12 |
C8 |
C |
C8 |
N |
Y |
N |
0 |
-0.873 |
-3.589 |
-0.687 |
13 |
N9 |
N |
N9 |
N |
Y |
N |
0 |
0.026 |
-2.626 |
-0.337 |
14 |
C1' |
C |
C1' |
R |
N |
N |
0 |
-0.254 |
-1.198 |
-0.17 |
15 |
C10 |
C |
C10 |
N |
N |
N |
0 |
1.508 |
2.952 |
-3.455 |
16 |
C11 |
C |
C11 |
N |
Y |
N |
0 |
2.286 |
3.475 |
-2.27 |
17 |
C12 |
C |
C12 |
N |
Y |
N |
0 |
1.969 |
2.652 |
-1.199 |
18 |
C13 |
C |
C13 |
N |
Y |
N |
0 |
3.165 |
4.523 |
-2.101 |
19 |
C14 |
C |
C14 |
N |
Y |
N |
0 |
3.729 |
4.758 |
-0.859 |
20 |
C15 |
C |
C15 |
N |
Y |
N |
0 |
3.413 |
3.944 |
0.212 |
21 |
C16 |
C |
C16 |
N |
Y |
N |
0 |
2.529 |
2.886 |
0.043 |
22 |
O17 |
O |
O17 |
N |
N |
N |
0 |
2.216 |
2.084 |
1.094 |
23 |
C18 |
C |
C18 |
N |
N |
N |
0 |
2.834 |
2.386 |
2.347 |
24 |
C19 |
C |
C19 |
N |
N |
N |
0 |
2.364 |
1.384 |
3.403 |
25 |
C2' |
C |
C2' |
R |
N |
N |
0 |
0.07 |
-0.432 |
-1.471 |
26 |
O2' |
O |
O2' |
N |
N |
N |
0 |
1.27 |
0.345 |
-1.262 |
27 |
C20 |
C |
C20 |
N |
N |
N |
0 |
3.025 |
1.708 |
4.744 |
28 |
O21 |
O |
O21 |
N |
N |
N |
0 |
2.586 |
0.771 |
5.73 |
29 |
C3' |
C |
C3' |
S |
N |
N |
0 |
-1.044 |
0.653 |
-1.551 |
30 |
O3' |
O |
O3' |
N |
N |
N |
0 |
-0.312 |
1.887 |
-1.375 |
31 |
C4' |
C |
C4' |
R |
N |
N |
0 |
-1.895 |
0.401 |
-0.288 |
32 |
O4' |
O |
O4' |
N |
N |
N |
0 |
-1.665 |
-0.985 |
0.045 |
33 |
C5' |
C |
C5' |
N |
N |
N |
0 |
-3.377 |
0.637 |
-0.589 |
34 |
O5' |
O |
O5' |
N |
N |
N |
0 |
-4.134 |
0.512 |
0.616 |
35 |
OP1 |
O |
OP1 |
N |
N |
N |
0 |
-6.229 |
0.619 |
2.201 |
36 |
OP2 |
O |
OP2 |
N |
N |
N |
0 |
-6.095 |
2.015 |
0.102 |
37 |
H2 |
H |
H2 |
N |
N |
N |
0 |
4.436 |
-3.323 |
0.522 |
38 |
HN6 |
H |
HN6 |
N |
N |
N |
0 |
2.733 |
-7.427 |
-0.506 |
39 |
HN6A |
H |
HN6A |
N |
N |
N |
0 |
1.101 |
-7.186 |
-0.827 |
40 |
H8 |
H |
H8 |
N |
N |
N |
0 |
-1.919 |
-3.415 |
-0.89 |
41 |
H1' |
H |
H1' |
N |
N |
N |
0 |
0.323 |
-0.793 |
0.661 |
42 |
H10 |
H |
H10 |
N |
N |
N |
0 |
2.143 |
2.934 |
-4.34 |
43 |
H10A |
H |
H10A |
N |
N |
N |
0 |
0.635 |
3.579 |
-3.634 |
44 |
H13 |
H |
H13 |
N |
N |
N |
0 |
3.413 |
5.16 |
-2.936 |
45 |
H14 |
H |
H14 |
N |
N |
N |
0 |
4.417 |
5.579 |
-0.727 |
46 |
H15 |
H |
H15 |
N |
N |
N |
0 |
3.853 |
4.13 |
1.18 |
47 |
H18 |
H |
H18 |
N |
N |
N |
0 |
3.917 |
2.323 |
2.243 |
48 |
H18A |
H |
H18A |
N |
N |
N |
0 |
2.557 |
3.395 |
2.655 |
49 |
H19 |
H |
H19 |
N |
N |
N |
0 |
1.28 |
1.447 |
3.507 |
50 |
H19A |
H |
H19A |
N |
N |
N |
0 |
2.641 |
0.375 |
3.095 |
51 |
H2' |
H |
H2' |
N |
N |
N |
0 |
0.125 |
-1.079 |
-2.347 |
52 |
H20 |
H |
H20 |
N |
N |
N |
0 |
4.108 |
1.644 |
4.64 |
53 |
H20A |
H |
H20A |
N |
N |
N |
0 |
2.748 |
2.716 |
5.052 |
54 |
HO21 |
H |
HO21 |
N |
N |
N |
0 |
2.966 |
0.916 |
6.607 |
55 |
H3' |
H |
H3' |
N |
N |
N |
0 |
-1.614 |
0.621 |
-2.479 |
56 |
H4' |
H |
H4' |
N |
N |
N |
0 |
-1.566 |
1.046 |
0.526 |
57 |
H5' |
H |
H5' |
N |
N |
N |
0 |
-3.509 |
1.638 |
-1.0 |
58 |
H5'A |
H |
H5'A |
N |
N |
N |
0 |
-3.722 |
-0.101 |
-1.313 |
59 |
HOP1 |
H |
HOP1 |
N |
N |
N |
0 |
-7.184 |
0.723 |
2.309 |
60 |
OP3 |
O |
OP3 |
N |
N |
Y |
0 |
-6.438 |
-0.469 |
-0.184 |
61 |
HOP3 |
H |
HOP3 |
N |
N |
N |
0 |
-6.243 |
-1.362 |
0.133 |
DJF : Chemical Bonds
Total Number of Bonds: 66
DJF : Used in PDB Entries
Total Number of PDB Entries: 1
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
DJF |
3zju |
Polymer component
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1 |
1 |
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