Chemical Components in the PDB

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365 : Summary

Code

365

One-letter code

X

Molecule name

[(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-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

Synonyms

3-AMINOMETHYL-7-(3-HYDROXY-PROPOXY)-3H-BENZO[C][1,2]OXABOROL-1-OL modified adenosine

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.6 [(1S,5R,6R,7'S,8R)-7'-(aminomethyl)-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

C21 H27 B N6 O10 P

Formal charge

-1

Molecular weight

565.258 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.370 NC[CH]1O[B-]2(O[CH]3[CH](CO[P](O)(O)=O)O[CH]([CH]3O2)n4cnc5c(N)ncnc45)c6c(OCCCO)cccc16
SMILES OpenEye OEToolkits 1.7.6 [B-]12(c3c(cccc3OCCCO)C(O1)CN)OC4C(OC(C4O2)n5cnc6c5ncnc6N)COP(=O)(O)O
Canonical SMILES CACTVS 3.370 NC[C@H]1O[B-]2(O[C@@H]3[C@@H](CO[P](O)(O)=O)O[C@H]([C@@H]3O2)n4cnc5c(N)ncnc45)c6c(OCCCO)cccc16
Canonical SMILES OpenEye OEToolkits 1.7.6 [B-]12(c3c(cccc3OCCCO)[C@H](O1)CN)O[C@@H]4[C@H](O[C@H]([C@@H]4O2)n5cnc6c5ncnc6N)COP(=O)(O)O

IUPAC InChI

InChI=1S/C21H27BN6O10P/c23-7-13-11-3-1-4-12(33-6-2-5-29)15(11)22(36-13)37-17-14(8-34-39(30,31)32)35-21(18(17)38-22)28-10-27-16-19(24)25-9-26-20(16)28/h1,3-4,9-10,13-14,17-18,21,29H,2,5-8,23H2,(H2,24,25,26)(H2,30,31,32)/q-1/p-2/t13-,14-,17-,18-,21-,22+/m1/s1

IUPAC InChI key

SQCWYVPZBCHHDX-ZKDXOGESSA-L
365

wwPDB Information

Atom count

66 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-01-21

Last modified at

2013-04-12

Status

Released

Obsoleted

Not Assigned



365 : Atoms of Molecule

Total Number of Atoms: 66
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O3P O O3P N N N 0 6.479 1.104 -1.806
2 B B B N N N -1 -1.304 1.454 1.095
3 P P P N N N 0 5.709 1.563 -0.468
4 N1 N N1 N Y N 0 -2.136 -5.651 0.366
5 O1 O O1 N N N 0 -1.603 1.673 2.415
6 C2 C C2 N Y N 0 -2.492 -4.477 -0.121
7 N3 N N3 N Y N 0 -1.69 -3.432 -0.104
8 C4 C C4 N Y N 0 -0.47 -3.524 0.414
9 C5 C C5 N Y N 0 -0.044 -4.754 0.945
10 C6 C C6 N Y N 0 -0.936 -5.839 0.904
11 N6 N N6 N N N 0 -0.572 -7.074 1.412
12 N7 N N7 N Y N 0 1.219 -4.576 1.401
13 C8 C C8 N Y N 0 1.587 -3.345 1.189
14 N9 N N9 N Y N 0 0.579 -2.656 0.582
15 C1' C C1' R N N 0 0.611 -1.247 0.182
16 C10 C C10 S N N 0 -2.296 2.934 2.459
17 C11 C C11 N Y N 0 -2.996 3.088 1.13
18 C12 C C12 N Y N 0 -2.396 2.183 0.264
19 C13 C C13 N Y N 0 -4.022 3.892 0.686
20 C14 C C14 N Y N 0 -4.454 3.802 -0.626
21 C15 C C15 N Y N 0 -3.857 2.906 -1.492
22 C16 C C16 N Y N 0 -2.824 2.093 -1.047
23 C17 C C17 N N N 0 -3.321 2.93 3.594
24 N18 N N18 N N N 0 -2.622 2.866 4.885
25 O19 O O19 N N N 0 -2.235 1.212 -1.898
26 O1P O O1P N N N 0 6.372 0.966 0.712
27 C2' C C2' R N N 0 -0.014 -0.363 1.282
28 O2' O O2' N N N 0 -1.299 0.109 0.819
29 C20 C C20 N N N 0 -2.729 1.174 -3.238
30 C21 C C21 N N N 0 -1.95 0.13 -4.04
31 C22 C C22 N N N 0 -2.479 0.09 -5.475
32 O23 O O23 N N N 0 -1.751 -0.885 -6.224
33 O2P O O2P N N N 0 5.748 3.168 -0.352
34 C3' C C3' S N N 0 0.861 0.925 1.265
35 O3' O O3' N N N 0 -0.055 1.938 0.795
36 C4' C C4' R N N 0 1.901 0.65 0.158
37 O4' O O4' N N N 0 1.975 -0.789 0.067
38 C5' C C5' N N N 0 3.262 1.229 0.551
39 O5' O O5' N N N 0 4.179 1.067 -0.533
40 H2 H H2 N N N 0 -3.477 -4.368 -0.55
41 HN6 H HN6 N N N 0 -1.197 -7.815 1.377
42 HN6A H HN6A N N N 0 0.307 -7.198 1.802
43 H8 H H8 N N N 0 2.548 -2.931 1.455
44 H1' H H1' N N N 0 0.082 -1.11 -0.761
45 H10 H H10 N N N 0 -1.583 3.746 2.602
46 H13 H H13 N N N 0 -4.49 4.593 1.362
47 H14 H H14 N N N 0 -5.259 4.433 -0.973
48 H15 H H15 N N N 0 -4.195 2.839 -2.516
49 H17 H H17 N N N 0 -3.918 3.841 3.549
50 H17A H H17A N N N 0 -3.974 2.062 3.491
51 HN18 H HN18 N N N 0 -1.963 3.624 4.977
52 HN1A H HN1A N N N 0 -3.279 2.862 5.652
53 H2' H H2' N N N 0 -0.062 -0.856 2.253
54 H20 H H20 N N N 0 -3.787 0.909 -3.228
55 H20A H H20A N N N 0 -2.605 2.154 -3.699
56 H21 H H21 N N N 0 -0.892 0.395 -4.05
57 H21A H H21A N N N 0 -2.074 -0.85 -3.579
58 H22 H H22 N N N 0 -3.536 -0.175 -5.465
59 H22A H H22A N N N 0 -2.355 1.07 -5.936
60 HO23 H HO23 N N N 0 -2.034 -0.965 -7.145
61 H3' H H3' N N N 0 1.302 1.162 2.234
62 H4' H H4' N N N 0 1.567 1.074 -0.789
63 H5' H H5' N N N 0 3.154 2.289 0.78
64 H5'A H H5'A N N N 0 3.64 0.705 1.429
65 HOP3 H HOP3 N N N 0 7.409 1.37 -1.836
66 HOP2 H HOP2 N N N 0 5.33 3.627 -1.093



365 : Chemical Bonds

Total Number of Bonds: 71
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3P P O P sing 1.6105356 N N
2 B O1 B O sing 1.3710442 N N
3 B C12 B C sing 1.5538552 N N
4 B O2' B O sing 1.3730353 N N
5 B O3' B O sing 1.3726825 N N
6 P O1P P O doub 1.4793167 N N
7 P O2P P O sing 1.609659 N N
8 P O5' P O sing 1.6097021 N N
9 N1 C2 N C doub 1.3199171 N Y
10 N1 C6 N C sing 1.3284532 N Y
11 O1 C10 O C sing 1.4395506 N N
12 C2 N3 C N sing 1.3173906 N Y
13 N3 C4 N C doub 1.3286037 N Y
14 C4 C5 C C sing 1.4058225 N Y
15 C4 N9 C N sing 1.3718779 N Y
16 C5 C6 C C doub 1.4051939 N Y
17 C5 N7 C N sing 1.3545438 N Y
18 C6 N6 C N sing 1.3841188 N N
19 N7 C8 N C doub 1.3022016 N Y
20 C8 N9 C N sing 1.3635373 N Y
21 N9 C1' N C sing 1.4650273 N N
22 C1' C2' C C sing 1.5433992 N N
23 C1' O4' C O sing 1.4434282 N N
24 C10 C11 C C sing 1.5099527 N N
25 C10 C17 C C sing 1.5293351 N N
26 C11 C12 C C doub 1.3888776 N Y
27 C11 C13 C C sing 1.377036 N Y
28 C12 C16 C C sing 1.3820293 N Y
29 C13 C14 C C doub 1.3842211 N Y
30 C14 C15 C C sing 1.3817312 N Y
31 C15 C16 C C doub 1.387834 N Y
32 C16 O19 C O sing 1.3591479 N N
33 C17 N18 C N sing 1.4694822 N N
34 O19 C20 O C sing 1.4286637 N N
35 C2' O2' C O sing 1.4451221 N N
36 C2' C3' C C sing 1.5571955 N N
37 C20 C21 C C sing 1.5296997 N N
38 C21 C22 C C sing 1.5299236 N N
39 C22 O23 C O sing 1.4288492 N N
40 C3' O3' C O sing 1.4443424 N N
41 C3' C4' C C sing 1.5435913 N N
42 C4' O4' C O sing 1.4437722 N N
43 C4' C5' C C sing 1.5303631 N N
44 C5' O5' C O sing 1.4290518 N N
45 C2 H2 C H sing 1.0798829 N N
46 N6 HN6 N H sing 0.970016 N N
47 N6 HN6A N H sing 0.9695963 N N
48 C8 H8 C H sing 1.0796634 N N
49 C1' H1' C H sing 1.0898894 N N
50 C10 H10 C H sing 1.0900284 N N
51 C13 H13 C H sing 1.0804633 N N
52 C14 H14 C H sing 1.0800903 N N
53 C15 H15 C H sing 1.0804207 N N
54 C17 H17 C H sing 1.090117 N N
55 C17 H17A C H sing 1.0910738 N N
56 N18 HN18 N H sing 1.0086174 N N
57 N18 HN1A N H sing 1.0099277 N N
58 C2' H2' C H sing 1.0900431 N N
59 C20 H20 C H sing 1.0907286 N N
60 C20 H20A C H sing 1.0900904 N N
61 C21 H21 C H sing 1.0907286 N N
62 C21 H21A C H sing 1.0900904 N N
63 C22 H22 C H sing 1.0897586 N N
64 C22 H22A C H sing 1.0900904 N N
65 O23 HO23 O H sing 0.96681434 N N
66 C3' H3' C H sing 1.0906929 N N
67 C4' H4' C H sing 1.0900187 N N
68 C5' H5' C H sing 1.0898188 N N
69 C5' H5'A C H sing 1.090112 N N
70 O3P HOP3 O H sing 0.96775824 N N
71 O2P HOP2 O H sing 0.96668816 N N



365 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
365 3zjv Open in New Window Polymer component 1 1