Chemical Components in the PDB

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N33 : Summary

Code

N33

One-letter code

X

Molecule name

(2S,3R,4R,5S,6R)-3-AMINO-4-({[(2S,3R,4R,5S,6R)-3-AMINO-2-{[(1R,2R,3S,4R,6S)-4,6-DIAMINO-2,3-DIHYDROXYCYCLOHEXYL]OXY}-5-HYDROXY-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-4-YL]OXY}METHOXY)-6-(HYDROXYMETHYL)TETRAHYDRO-2H-PYRAN-2,5-DIOL

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S,3R,4R,5S,6R)-3-amino-4-({[(2S,3R,4R,5S,6R)-3-amino-2-{[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxycyclohexyl]oxy}-5-hydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-4-yl]oxy}methoxy)-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diol (non-preferred name)
OpenEye OEToolkits 1.5.0 (2S,3R,4R,5S,6R)-3-amino-4-[[(2S,3R,4R,5S,6R)-3-amino-2-[(1R,2R,3S,4R,6S)-4,6-diamino-2,3-dihydroxy-cyclohexyl]oxy-5-hydroxy-6-(hydroxymethyl)oxan-4-yl]oxymethoxy]-6-(hydroxymethyl)oxane-2,5-diol

Formula

C19 H38 N4 O12

Formal charge

0

Molecular weight

514.525 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O(C1C(O)C(O)C(N)CC1N)C3OC(C(O)C(OCOC2C(N)C(O)OC(CO)C2O)C3N)CO
SMILES CACTVS 3.341 N[CH]1C[CH](N)[CH](O[CH]2O[CH](CO)[CH](O)[CH](OCO[CH]3[CH](N)[CH](O)O[CH](CO)[CH]3O)[CH]2N)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)OCOC3C(C(OC(C3O)CO)O)N)N)O)O)N
Canonical SMILES CACTVS 3.341 N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](OCO[C@@H]3[C@@H](N)[C@@H](O)O[C@H](CO)[C@H]3O)[C@H]2N)[C@H](O)[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)OCO[C@@H]3[C@H]([C@H](O[C@@H]([C@H]3O)CO)O)N)N)O)O)N

IUPAC InChI

InChI=1S/C19H38N4O12/c20-5-1-6(21)15(14(29)11(5)26)35-19-10(23)17(13(28)8(3-25)34-19)32-4-31-16-9(22)18(30)33-7(2-24)12(16)27/h5-19,24-30H,1-4,20-23H2/t5-,6+,7-,8-,9-,10-,11+,12-,13-,14-,15-,16-,17-,18+,19-/m1/s1

IUPAC InChI key

BKAACSMFIQVWGC-LZHQQFSOSA-N
N33

wwPDB Information

Atom count

73 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAD

Is modified

No

Standard parent

Not Assigned

Defined at

2007-01-12

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



N33 : Atoms of Molecule

Total Number of Atoms: 73
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C11 C C11 S N N 0 1.37 2.611 1.828
2 O11 O O11 N N N 0 2.406 3.552 1.554
3 C21 C C21 R N N 0 1.297 1.601 0.676
4 N21 N N21 N N N 0 1.148 2.27 -0.6
5 C31 C C31 R N N 0 0.157 0.6 0.905
6 O31 O O31 N N N 0 0.523 -0.304 1.947
7 C41 C C41 S N N 0 -1.154 1.294 1.291
8 O41 O O41 N N N 0 -1.709 1.864 0.102
9 C51 C C51 R N N 0 -0.979 2.416 2.329
10 O51 O O51 N N N 0 0.119 3.275 1.999
11 C61 C C61 N N N 0 -0.872 1.912 3.767
12 O61 O O61 N N N 0 -0.704 3.026 4.623
13 C12 C C12 R N N 0 3.949 6.879 3.678
14 N12 N N12 N N N 0 4.129 7.892 4.722
15 C22 C C22 N N N 0 2.531 6.991 3.11
16 C32 C C32 S N N 0 2.275 5.919 2.048
17 N32 N N32 N N N 0 0.894 6.03 1.572
18 C42 C C42 R N N 0 2.525 4.512 2.608
19 C52 C C52 R N N 0 3.921 4.381 3.227
20 O52 O O52 N N N 0 3.984 3.108 3.879
21 C62 C C62 S N N 0 4.214 5.481 4.253
22 O62 O O62 N N N 0 5.594 5.404 4.621
23 C13 C C13 S N N 0 2.113 -4.669 1.293
24 O13 O O13 N N N 0 2.355 -5.576 2.368
25 C23 C C23 R N N 0 0.929 -3.766 1.661
26 N23 N N23 N N N 0 -0.233 -4.548 2.03
27 C33 C C33 R N N 0 0.6 -2.809 0.507
28 O33 O O33 N N N 0 1.607 -1.802 0.426
29 C43 C C43 S N N 0 0.516 -3.534 -0.841
30 O43 O O43 N N N 0 -0.733 -4.231 -0.88
31 C53 C C53 R N N 0 1.645 -4.553 -1.068
32 O53 O O53 N N N 0 1.851 -5.379 0.084
33 C63 C C63 N N N 0 2.956 -3.923 -1.536
34 H21 H H21 N N N 0 2.252 1.062 0.644
35 O63 O O63 N N N 0 2.723 -3.265 -2.768
36 C77 C C77 N N N 0 1.703 -1.036 1.626
37 H11 H H11 N N N 0 1.642 2.111 2.764
38 H211 H 1H21 N N N 0 0.76 3.186 -0.602
39 H212 H 2H21 N N N 0 1.243 1.722 -1.426
40 H31 H H31 N N N 0 0.01 -0.008 0.004
41 H41 H H41 N N N 0 -1.881 0.562 1.662
42 HO41 H HO41 N N N 0 -1.164 2.637 -0.113
43 H51 H H51 N N N 0 -1.866 3.059 2.29
44 H611 H 1H61 N N N 0 -0.013 1.248 3.865
45 H612 H 2H61 N N N 0 -1.782 1.379 4.042
46 HO61 H HO61 N N N 0 -0.769 3.824 4.07
47 H12 H H12 N N N 0 4.679 7.094 2.889
48 H121 H 1H12 N N N 0 4.534 7.604 5.584
49 H122 H 2H12 N N N 0 3.662 8.763 4.609
50 H221 H 1H22 N N N 0 1.797 6.894 3.922
51 H222 H 2H22 N N N 0 2.386 7.988 2.672
52 H32 H H32 N N N 0 2.93 6.089 1.185
53 H321 H 1H32 N N N 0 0.479 6.934 1.561
54 H322 H 2H32 N N N 0 0.368 5.192 1.477
55 H42 H H42 N N N 0 1.765 4.251 3.355
56 H52 H H52 N N N 0 4.691 4.36 2.447
57 HO52 H HO52 N N N 0 3.49 2.492 3.319
58 H62 H H62 N N N 0 3.63 5.308 5.165
59 HO62 H HO62 N N N 0 5.691 4.593 5.141
60 H13 H H13 N N N 0 3.027 -4.078 1.172
61 HO13 H HO13 N N N 0 1.485 -5.87 2.681
62 H23 H H23 N N N 0 1.215 -3.184 2.545
63 H231 H 1H23 N N N 0 -0.091 -5.498 2.288
64 H232 H 2H23 N N N 0 -1.131 -4.175 1.817
65 H33 H H33 N N N 0 -0.343 -2.289 0.715
66 H43 H H43 N N N 0 0.503 -2.812 -1.665
67 HO43 H HO43 N N N 0 -0.651 -4.98 -0.269
68 H53 H H53 N N N 0 1.33 -5.241 -1.86
69 H631 H 1H63 N N N 0 3.71 -4.697 -1.677
70 H632 H 2H63 N N N 0 3.304 -3.199 -0.8
71 HO63 H HO63 N N N 0 2.781 -3.939 -3.467
72 H771 H 1H77 N N N 0 1.95 -1.716 2.449
73 H772 H 2H77 N N N 0 2.53 -0.322 1.541



N33 : Chemical Bonds

Total Number of Bonds: 75
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 1.1 N N
5 O11 C42 O C sing 1.43 N N
6 C21 N21 C N sing 1.45 N N
7 C21 C31 C C sing 1.53 N N
8 C21 H21 C H sing 1.1 N N
9 N21 H211 N H sing 0.99 N N
10 N21 H212 N H sing 1.0 N N
11 C31 O31 C O sing 1.43 N N
12 C31 C41 C C sing 1.53 N N
13 C31 H31 C H sing 1.1 N N
14 O31 C77 O C sing 1.43 N N
15 C41 C51 C C sing 1.54 N N
16 C41 O41 C O sing 1.43 N N
17 C41 H41 C H sing 1.1 N N
18 O41 HO41 O H sing 0.97 N N
19 C51 O51 C O sing 1.43 N N
20 C51 C61 C C sing 1.53 N N
21 C51 H51 C H sing 1.1 N N
22 C61 O61 C O sing 1.41 N N
23 C61 H611 C H sing 1.09 N N
24 C61 H612 C H sing 1.09 N N
25 O61 HO61 O H sing 0.97 N N
26 C12 N12 C N sing 1.47 N N
27 C12 C62 C C sing 1.53 N N
28 C12 C22 C C sing 1.53 N N
29 C12 H12 C H sing 1.1 N N
30 N12 H121 N H sing 0.99 N N
31 N12 H122 N H sing 0.99 N N
32 C22 C32 C C sing 1.53 N N
33 C22 H221 C H sing 1.1 N N
34 C22 H222 C H sing 1.1 N N
35 C32 C42 C C sing 1.53 N N
36 C32 N32 C N sing 1.46 N N
37 C32 H32 C H sing 1.1 N N
38 N32 H321 N H sing 0.99 N N
39 N32 H322 N H sing 0.99 N N
40 C42 C52 C C sing 1.53 N N
41 C42 H42 C H sing 1.1 N N
42 C52 C62 C C sing 1.53 N N
43 C52 O52 C O sing 1.43 N N
44 C52 H52 C H sing 1.1 N N
45 O52 HO52 O H sing 0.97 N N
46 C62 O62 C O sing 1.43 N N
47 C62 H62 C H sing 1.1 N N
48 O62 HO62 O H sing 0.97 N N
49 C13 C23 C C sing 1.53 N N
50 C13 O53 C O sing 1.43 N N
51 C13 O13 C O sing 1.43 N N
52 C13 H13 C H sing 1.1 N N
53 O13 HO13 O H sing 0.97 N N
54 C23 C33 C C sing 1.53 N N
55 C23 N23 C N sing 1.45 N N
56 C23 H23 C H sing 1.1 N N
57 N23 H231 N H sing 0.99 N N
58 N23 H232 N H sing 1.0 N N
59 C33 O33 C O sing 1.43 N N
60 C33 C43 C C sing 1.53 N N
61 C33 H33 C H sing 1.1 N N
62 O33 C77 O C sing 1.43 N N
63 C43 O43 C O sing 1.43 N N
64 C43 C53 C C sing 1.54 N N
65 C43 H43 C H sing 1.1 N N
66 O43 HO43 O H sing 0.97 N N
67 C53 C63 C C sing 1.53 N N
68 C53 O53 C O sing 1.43 N N
69 C53 H53 C H sing 1.1 N N
70 C63 O63 C O sing 1.42 N N
71 C63 H631 C H sing 1.09 N N
72 C63 H632 C H sing 1.09 N N
73 O63 HO63 O H sing 0.97 N N
74 C77 H771 C H sing 1.1 N N
75 C77 H772 C H sing 1.1 N N



N33 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
N33 2o3v Open in New Window Bound ligand 1 1