Chemical Components in the PDB

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DJF : Summary

Code

DJF

One-letter code

X

Molecule name

[(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

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.6 [(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

Formula

C20 H24 B N5 O10 P

Formal charge

-1

Molecular weight

536.217 Da

SMILES

TypeProgramVersionDescriptor
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

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
DJF

wwPDB Information

Atom count

61 (37 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-01-21

Last modified at

2013-04-12

Status

Released

Obsoleted

Not Assigned



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 C1' C C1' R N N 0 -0.254 -1.198 -0.17
3 C10 C C10 N N N 0 1.508 2.952 -3.455
4 C11 C C11 N Y N 0 2.286 3.475 -2.27
5 C12 C C12 N Y N 0 1.969 2.652 -1.199
6 C13 C C13 N Y N 0 3.165 4.523 -2.101
7 C14 C C14 N Y N 0 3.729 4.758 -0.859
8 C15 C C15 N Y N 0 3.413 3.944 0.212
9 C16 C C16 N Y N 0 2.529 2.886 0.043
10 C18 C C18 N N N 0 2.834 2.386 2.347
11 C19 C C19 N N N 0 2.364 1.384 3.403
12 C2 C C2 N Y N 0 3.457 -3.688 0.249
13 C2' C C2' R N N 0 0.07 -0.432 -1.471
14 C20 C C20 N N N 0 3.025 1.708 4.744
15 C3' C C3' S N N 0 -1.044 0.653 -1.551
16 C4 C C4 N Y N 0 1.241 -3.24 -0.168
17 C4' C C4' R N N 0 -1.895 0.401 -0.288
18 C5 C C5 N Y N 0 1.026 -4.603 -0.432
19 C5' C C5' N N N 0 -3.377 0.637 -0.589
20 C6 C C6 N Y N 0 2.121 -5.479 -0.33
21 C8 C C8 N Y N 0 -0.873 -3.589 -0.687
22 H1' H H1' N N N 0 0.323 -0.793 0.661
23 H10 H H10 N N N 0 2.143 2.934 -4.34
24 H10A H H10A N N N 0 0.635 3.579 -3.634
25 H13 H H13 N N N 0 3.413 5.16 -2.936
26 H14 H H14 N N N 0 4.417 5.579 -0.727
27 H15 H H15 N N N 0 3.853 4.13 1.18
28 H18 H H18 N N N 0 3.917 2.323 2.243
29 H18A H H18A N N N 0 2.557 3.395 2.655
30 H19 H H19 N N N 0 1.28 1.447 3.507
31 H19A H H19A N N N 0 2.641 0.375 3.095
32 H2 H H2 N N N 0 4.436 -3.323 0.522
33 H2' H H2' N N N 0 0.125 -1.079 -2.347
34 H20 H H20 N N N 0 4.108 1.644 4.64
35 H20A H H20A N N N 0 2.748 2.716 5.052
36 H3' H H3' N N N 0 -1.614 0.621 -2.479
37 H4' H H4' N N N 0 -1.566 1.046 0.526
38 H5' H H5' N N N 0 -3.509 1.638 -1.0
39 H5'A H H5'A N N N 0 -3.722 -0.101 -1.313
40 H8 H H8 N N N 0 -1.919 -3.415 -0.89
41 HN6 H HN6 N N N 0 2.733 -7.427 -0.506
42 HN6A H HN6A N N N 0 1.101 -7.186 -0.827
43 HO21 H HO21 N N N 0 2.966 0.916 6.607
44 HOP1 H HOP1 N N N 0 -7.184 0.723 2.309
45 HOP3 H HOP3 N N N 0 -6.243 -1.362 0.133
46 N1 N N1 N Y N 0 3.304 -4.978 0.01
47 N3 N N3 N Y N 0 2.461 -2.831 0.166
48 N6 N N6 N N N 0 1.97 -6.832 -0.579
49 N7 N N7 N Y N 0 -0.284 -4.748 -0.742
50 N9 N N9 N Y N 0 0.026 -2.626 -0.337
51 O1 O O1 N N N 0 1.095 1.616 -3.116
52 O17 O O17 N N N 0 2.216 2.084 1.094
53 O2' O O2' N N N 0 1.27 0.345 -1.262
54 O21 O O21 N N N 0 2.586 0.771 5.73
55 O3' O O3' N N N 0 -0.312 1.887 -1.375
56 O4' O O4' N N N 0 -1.665 -0.985 0.045
57 O5' O O5' N N N 0 -4.134 0.512 0.616
58 OP1 O OP1 N N N 0 -6.229 0.619 2.201
59 OP2 O OP2 N N N 0 -6.095 2.015 0.102
60 OP3 O OP3 N N Y 0 -6.438 -0.469 -0.184
61 P P P N N N 0 -5.732 0.698 0.671



DJF : Chemical Bonds

Total Number of Bonds: 66
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 B O1 B O sing 1.37 N N
2 B C12 B C sing 1.55 N N
3 B O2' B O sing 1.37 N N
4 B O3' B O sing 1.37 N N
5 P O5' P O sing 1.61 N N
6 P OP1 P O sing 1.61 N N
7 P OP2 P O doub 1.48 N N
8 N1 C2 N C doub 1.32 N Y
9 N1 C6 N C sing 1.33 N Y
10 O1 C10 O C sing 1.44 N N
11 C2 N3 C N sing 1.32 N Y
12 N3 C4 N C doub 1.33 N Y
13 C4 C5 C C sing 1.4 N Y
14 C4 N9 C N sing 1.37 N Y
15 C5 C6 C C doub 1.41 N Y
16 C5 N7 C N sing 1.35 N Y
17 C6 N6 C N sing 1.38 N N
18 N7 C8 N C doub 1.3 N Y
19 C8 N9 C N sing 1.36 N Y
20 N9 C1' N C sing 1.46 N N
21 C1' C2' C C sing 1.54 N N
22 C1' O4' C O sing 1.44 N N
23 C10 C11 C C sing 1.51 N N
24 C11 C12 C C doub 1.39 N Y
25 C11 C13 C C sing 1.38 N Y
26 C12 C16 C C sing 1.38 N Y
27 C13 C14 C C doub 1.38 N Y
28 C14 C15 C C sing 1.38 N Y
29 C15 C16 C C doub 1.39 N Y
30 C16 O17 C O sing 1.36 N N
31 O17 C18 O C sing 1.43 N N
32 C18 C19 C C sing 1.53 N N
33 C19 C20 C C sing 1.53 N N
34 C2' O2' C O sing 1.44 N N
35 C2' C3' C C sing 1.56 N N
36 C20 O21 C O sing 1.43 N N
37 C3' O3' C O sing 1.45 N N
38 C3' C4' C C sing 1.54 N N
39 C4' O4' C O sing 1.44 N N
40 C4' C5' C C sing 1.53 N N
41 C5' O5' C O sing 1.43 N N
42 C2 H2 C H sing 1.08 N N
43 N6 HN6 N H sing 0.97 N N
44 N6 HN6A N H sing 0.97 N N
45 C8 H8 C H sing 1.08 N N
46 C1' H1' C H sing 1.09 N N
47 C10 H10 C H sing 1.09 N N
48 C10 H10A C H sing 1.09 N N
49 C13 H13 C H sing 1.08 N N
50 C14 H14 C H sing 1.08 N N
51 C15 H15 C H sing 1.08 N N
52 C18 H18 C H sing 1.09 N N
53 C18 H18A C H sing 1.09 N N
54 C19 H19 C H sing 1.09 N N
55 C19 H19A C H sing 1.09 N N
56 C2' H2' C H sing 1.09 N N
57 C20 H20 C H sing 1.09 N N
58 C20 H20A C H sing 1.09 N N
59 O21 HO21 O H sing 0.97 N N
60 C3' H3' C H sing 1.09 N N
61 C4' H4' C H sing 1.09 N N
62 C5' H5' C H sing 1.09 N N
63 C5' H5'A C H sing 1.09 N N
64 HOP1 OP1 H O sing 0.97 N N
65 P OP3 P O sing 1.61 N N
66 HOP3 OP3 H O sing 0.97 N N



DJF : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
DJF 3zju Open in New Window Polymer component 1 1