Chemical Components in the PDB

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TOY : Summary

Code

TOY

One-letter code

X

Molecule name

TOBRAMYCIN

Synonyms

4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL

Systematic names

ProgramVersionName
ACDLabs 10.04 (1S,2S,3R,4S,6R)-4,6-diamino-3-[(2,6-diamino-2,3,6-trideoxy-alpha-D-ribo-hexopyranosyl)oxy]-2-hydroxycyclohexyl 3-amino-3-deoxy-alpha-D-glucopyranoside
OpenEye OEToolkits 1.5.0 (2S,3R,4S,5S,6R)-4-amino-2-[(1S,2S,3R,4S,6R)-4,6-diamino-3-[(2R,3R,5S,6R)-3-amino-6-(aminomethyl)-5-hydroxy-oxan-2-yl]oxy-2-hydroxy-cyclohexyl]oxy-6-(hydroxymethyl)oxane-3,5-diol

Formula

C18 H37 N5 O9

Formal charge

0

Molecular weight

467.514 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O(C2C(O)C(OC1OC(CN)C(O)CC1N)C(N)CC2N)C3OC(C(O)C(N)C3O)CO
SMILES CACTVS 3.341 NC[CH]1O[CH](O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O)[CH]2O)[CH](N)C[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)N)O)O)OC3C(CC(C(O3)CN)O)N)N
Canonical SMILES CACTVS 3.341 NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O)[C@H]2O)[C@H](N)C[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)N)O)O)O[C@@H]3[C@@H](C[C@@H]([C@H](O3)CN)O)N)N

IUPAC InChI

InChI=1S/C18H37N5O9/c19-3-9-8(25)2-7(22)17(29-9)31-15-5(20)1-6(21)16(14(15)28)32-18-13(27)11(23)12(26)10(4-24)30-18/h5-18,24-28H,1-4,19-23H2/t5-,6+,7+,8-,9+,10+,11-,12+,13+,14-,15+,16-,17+,18+/m0/s1

IUPAC InChI key

NLVFBUXFDBBNBW-PBSUHMDJSA-N
TOY

wwPDB Information

Atom count

69 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAD

Is modified

No

Standard parent

Not Assigned

Defined at

2002-04-09

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



TOY : Atoms of Molecule

Total Number of Atoms: 69
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C11 C C11 R N N 0 -1.142 -0.196 -2.574
2 O11 O O11 N N N 0 0.028 -0.989 -2.371
3 C21 C C21 R N N 0 -2.181 -1.012 -3.346
4 N21 N N21 N N N 0 -2.551 -2.2 -2.565
5 C31 C C31 N N N 0 -1.58 -1.445 -4.688
6 C41 C C41 S N N 0 -1.058 -0.2 -5.414
7 O41 O O41 N N N 0 -0.362 -0.593 -6.598
8 C51 C C51 R N N 0 -0.102 0.554 -4.486
9 O51 O O51 N N N 0 -0.799 0.973 -3.315
10 C61 C C61 N N N 0 0.451 1.78 -5.215
11 N61 N N61 N N N 0 1.371 2.503 -4.326
12 C12 C C12 R N N 0 2.642 -0.465 0.915
13 N12 N N12 N N N 0 3.431 0.201 1.959
14 C22 C C22 N N N 0 3.1 0.022 -0.46
15 C32 C C32 S N N 0 2.277 -0.671 -1.547
16 N32 N N32 N N N 0 2.717 -0.203 -2.868
17 C42 C C42 R N N 0 0.796 -0.341 -1.356
18 C52 C C52 S N N 0 0.338 -0.829 0.019
19 O52 O O52 N N N 0 -1.045 -0.52 0.198
20 C62 C C62 S N N 0 1.16 -0.134 1.107
21 O62 O O62 N N N 0 0.732 -0.59 2.392
22 C13 C C13 S N N 0 0.951 0.485 3.306
23 C23 C C23 R N N 0 0.886 -0.043 4.74
24 O23 O O23 N N N 0 1.91 -1.021 4.936
25 C33 C C33 S N N 0 -0.484 -0.683 4.976
26 N33 N N33 N N N 0 -0.621 -1.059 6.389
27 C43 C C43 S N N 0 -1.569 0.334 4.607
28 O43 O O43 N N N 0 -2.854 -0.286 4.677
29 C53 C C53 R N N 0 -1.32 0.835 3.183
30 O53 O O53 N N N 0 -0.05 1.482 3.114
31 C63 C C63 N N N 0 -2.418 1.828 2.795
32 O63 O O63 N N N 0 -2.245 2.221 1.432
33 H11 H H11 N N N 0 -1.554 0.094 -1.608
34 H21 H H21 N N N 0 -3.067 -0.402 -3.523
35 HN21 H 1HN2 N N N 0 -3.234 -2.704 -3.111
36 HN22 H 2HN2 N N N 0 -1.729 -2.784 -2.518
37 H311 H 1H31 N N N 0 -0.758 -2.139 -4.514
38 H312 H 2H31 N N N 0 -2.347 -1.926 -5.294
39 H41 H H41 N N N 0 -1.895 0.444 -5.68
40 H41O H OH41 N N N 0 -0.997 -1.071 -7.15
41 H51 H H51 N N N 0 0.72 -0.101 -4.203
42 H611 H 1H61 N N N 0 -0.37 2.436 -5.499
43 H612 H 2H61 N N N 0 0.986 1.46 -6.109
44 HN61 H 1HN6 N N N 0 1.71 3.299 -4.846
45 HN62 H 2HN6 N N N 0 0.814 2.867 -3.568
46 H12 H H12 N N N 0 2.785 -1.543 0.984
47 HN11 H 1HN1 N N N 0 4.396 -0.043 1.794
48 HN12 H 2HN1 N N N 0 3.352 1.193 1.794
49 H221 H 1H22 N N N 0 4.155 -0.212 -0.596
50 H222 H 2H22 N N N 0 2.956 1.101 -0.529
51 H32 H H32 N N N 0 2.421 -1.75 -1.478
52 HN1 H 1HN N N N 0 3.723 -0.277 -2.882
53 HN2 H 2HN N N N 0 2.368 -0.867 -3.542
54 H42 H H42 N N N 0 0.653 0.737 -1.425
55 H52 H H52 N N N 0 0.481 -1.907 0.088
56 H52O H OH52 N N N 0 -1.325 -0.955 1.015
57 H62 H H62 N N N 0 1.017 0.943 1.037
58 H13 H H13 N N N 0 1.934 0.921 3.124
59 H23 H H23 N N N 0 1.029 0.779 5.44
60 H23O H OH23 N N N 0 2.754 -0.577 4.778
61 H33 H H33 N N N 0 -0.587 -1.57 4.35
62 HN31 H 1HN3 N N N 0 0.11 -1.726 6.584
63 HN32 H 2HN3 N N N 0 -0.411 -0.233 6.93
64 H43 H H43 N N N 0 -1.532 1.174 5.301
65 H43O H OH43 N N N 0 -3.504 0.386 4.432
66 H53 H H53 N N N 0 -1.335 -0.008 2.494
67 H631 H 1H63 N N N 0 -3.393 1.356 2.916
68 H632 H 2H63 N N N 0 -2.357 2.707 3.437
69 H63O H OH63 N N N 0 -2.905 2.903 1.252



TOY : 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 C11 O11 C O sing 1.43 N N
2 C11 C21 C C sing 1.53 N N
3 C11 O51 C O sing 1.43 N N
4 C11 H11 C H sing 1.09 N N
5 O11 C42 O C sing 1.43 N N
6 C21 N21 C N sing 1.47 N N
7 C21 C31 C C sing 1.53 N N
8 C21 H21 C H sing 1.09 N N
9 N21 HN21 N H sing 1.01 N N
10 N21 HN22 N H sing 1.01 N N
11 C31 C41 C C sing 1.53 N N
12 C31 H311 C H sing 1.09 N N
13 C31 H312 C H sing 1.09 N N
14 C41 O41 C O sing 1.43 N N
15 C41 C51 C C sing 1.53 N N
16 C41 H41 C H sing 1.09 N N
17 O41 H41O O H sing 0.97 N N
18 C51 O51 C O sing 1.43 N N
19 C51 C61 C C sing 1.53 N N
20 C51 H51 C H sing 1.09 N N
21 C61 N61 C N sing 1.47 N N
22 C61 H611 C H sing 1.09 N N
23 C61 H612 C H sing 1.09 N N
24 N61 HN61 N H sing 1.01 N N
25 N61 HN62 N H sing 1.01 N N
26 C12 N12 C N sing 1.47 N N
27 C12 C22 C C sing 1.53 N N
28 C12 C62 C C sing 1.53 N N
29 C12 H12 C H sing 1.09 N N
30 N12 HN11 N H sing 1.01 N N
31 N12 HN12 N H sing 1.01 N N
32 C22 C32 C C sing 1.53 N N
33 C22 H221 C H sing 1.09 N N
34 C22 H222 C H sing 1.09 N N
35 C32 N32 C N sing 1.47 N N
36 C32 C42 C C sing 1.53 N N
37 C32 H32 C H sing 1.09 N N
38 N32 HN1 N H sing 1.01 N N
39 N32 HN2 N H sing 1.01 N N
40 C42 C52 C C sing 1.53 N N
41 C42 H42 C H sing 1.09 N N
42 C52 O52 C O sing 1.43 N N
43 C52 C62 C C sing 1.53 N N
44 C52 H52 C H sing 1.09 N N
45 O52 H52O O H sing 0.97 N N
46 C62 O62 C O sing 1.43 N N
47 C62 H62 C H sing 1.09 N N
48 O62 C13 O C sing 1.43 N N
49 C13 C23 C C sing 1.53 N N
50 C13 O53 C O sing 1.43 N N
51 C13 H13 C H sing 1.09 N N
52 C23 O23 C O sing 1.43 N N
53 C23 C33 C C sing 1.53 N N
54 C23 H23 C H sing 1.09 N N
55 O23 H23O O H sing 0.97 N N
56 C33 N33 C N sing 1.47 N N
57 C33 C43 C C sing 1.53 N N
58 C33 H33 C H sing 1.09 N N
59 N33 HN31 N H sing 1.01 N N
60 N33 HN32 N H sing 1.01 N N
61 C43 O43 C O sing 1.43 N N
62 C43 C53 C C sing 1.53 N N
63 C43 H43 C H sing 1.09 N N
64 O43 H43O O H sing 0.97 N N
65 C53 O53 C O sing 1.43 N N
66 C53 C63 C C sing 1.53 N N
67 C53 H53 C H sing 1.09 N N
68 C63 O63 C O sing 1.43 N N
69 C63 H631 C H sing 1.09 N N
70 C63 H632 C H sing 1.09 N N
71 O63 H63O O H sing 0.97 N N



TOY : Used in PDB Entries

Total Number of PDB Entries: 13
Ligand Code PDB Entry ID Type Total Distinct
TOY 1lc4 Open in New Window Bound ligand 2 1
TOY 1m4d Open in New Window Bound ligand 2 1
TOY 3sg8 Open in New Window Bound ligand 2 1
TOY 3vet Open in New Window Bound ligand 1 1
TOY 4ebk Open in New Window Bound ligand 2 1
TOY 4evy Open in New Window Bound ligand 2 1
TOY 4jd6 Open in New Window Bound ligand 2 1
TOY 4lfc Open in New Window Bound ligand 1 1
TOY 4xje Open in New Window Bound ligand 1 1
TOY 5cfs Open in New Window Bound ligand 1 1
TOY 6np4 Open in New Window Bound ligand 1 1
TOY 7uuk Open in New Window Bound ligand 3 1
TOY 7uuo Open in New Window Bound ligand 3 1