Chemical Components in the PDB

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827 : Summary

Code

827

One-letter code

X

Molecule name

(1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2S,3S,4R,6S)-4,6-diamino-3-{[3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranosyl]oxy}-2-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside
OpenEye OEToolkits 2.0.6 (2~{R},3~{R},4~{R},5~{R})-2-[(1~{S},2~{S},3~{R},4~{S},6~{R})-4,6-bis(azanyl)-3-[(2~{S},3~{R},4~{R},5~{S},6~{R})-3-azanyl-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-2-oxidanyl-cyclohexyl]oxy-5-methyl-4-(methylamino)oxane-3,5-diol

Formula

C19 H38 N4 O10

Formal charge

0

Molecular weight

482.526 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1(C(C(O)C(C(CO)O1)O)N)OC2C(N)CC(C(C2O)OC3OCC(O)(C)C(C3O)NC)N
SMILES CACTVS 3.385 CN[CH]1[CH](O)[CH](OC[C]1(C)O)O[CH]2[CH](N)C[CH](N)[CH](O[CH]3O[CH](CO)[CH](O)[CH](O)[CH]3N)[CH]2O
SMILES OpenEye OEToolkits 2.0.6 CC1(COC(C(C1NC)O)OC2C(CC(C(C2O)OC3C(C(C(C(O3)CO)O)O)N)N)N)O
Canonical SMILES CACTVS 3.385 CN[C@@H]1[C@@H](O)[C@H](OC[C@]1(C)O)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](O)[C@H]3N)[C@@H]2O
Canonical SMILES OpenEye OEToolkits 2.0.6 C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H](C[C@@H]([C@H]([C@@H]2O)O[C@@H]3[C@@H]([C@H]([C@@H]([C@H](O3)CO)O)O)N)N)N)O

IUPAC InChI

InChI=1S/C19H38N4O10/c1-19(29)5-30-18(13(28)16(19)23-2)33-15-7(21)3-6(20)14(12(15)27)32-17-9(22)11(26)10(25)8(4-24)31-17/h6-18,23-29H,3-5,20-22H2,1-2H3/t6-,7+,8+,9+,10+,11+,12-,13+,14+,15-,16+,17+,18+,19-/m0/s1

IUPAC InChI key

HFLKNINDVFJPQT-ZFAMMYHGSA-N
827

wwPDB Information

Atom count

71 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-12-15

Last modified at

2017-10-27

Status

Released

Obsoleted

Not Assigned



827 : Atoms of Molecule

Total Number of Atoms: 71
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C14 N N N 0 4.637 2.951 -1.148
2 C02 C C6 R N N 0 4.641 1.422 -1.204
3 C04 C C7 N N N 0 3.281 0.925 -1.703
4 C06 C C8 R N N 0 3.458 -1.088 -0.411
5 C08 C C17 S N N 0 1.14 -1.182 0.193
6 C09 C C12 S N N 0 0.06 -0.191 0.632
7 C11 C C9 R N N 0 -1.321 -0.776 0.332
8 C13 C C1 S N N 0 -2.694 1.095 -0.266
9 C15 C C2 R N N 0 -4.652 -0.182 -0.804
10 C16 C C15 N N N 0 -5.367 -0.873 -1.967
11 C18 C C10 S N N 0 -5.571 0.882 -0.199
12 C20 C C3 R N N 0 -4.827 1.61 0.925
13 C22 C C4 R N N 0 -3.535 2.21 0.361
14 C24 C C5 S N N 0 -1.494 -2.091 1.096
15 C26 C C16 N N N 0 -0.414 -3.082 0.658
16 C27 C C11 R N N 0 0.967 -2.496 0.957
17 C29 C C18 R N N 0 4.825 -0.672 0.139
18 C31 C C13 R N N 0 4.9 0.857 0.196
19 C33 C C19 N N N 0 6.307 1.285 2.119
20 H1 H H1 N N N 0 -1.794 1.522 -0.706
21 H10 H H10 N N N 0 -4.949 -2.427 -3.196
22 H11 H H11 N N N 0 -5.857 1.598 -0.97
23 H12 H H12 N N N 0 1.058 -2.31 2.027
24 H13 H H13 N N N 0 0.152 -0.0040 1.702
25 H14 H H14 N N N 0 4.146 1.234 0.886
26 H15 H H15 N N N 0 4.449 3.351 -2.144
27 H16 H H16 N N N 0 3.854 3.287 -0.468
28 H17 H H17 N N N 0 5.604 3.303 -0.791
29 H18 H H18 N N N 0 -6.323 -1.269 -1.622
30 H19 H H19 N N N 0 -5.541 -0.153 -2.766
31 H2 H H2 N N N 0 -4.4 -0.92 -0.043
32 H20 H H20 N N N 0 -0.538 -4.018 1.202
33 H21 H H21 N N N 0 -0.506 -3.269 -0.412
34 H22 H H22 N N N 0 1.049 -1.369 -0.877
35 H23 H H23 N N N 0 1.033 1.515 0.139
36 H24 H H24 N N N 0 5.611 -1.051 -0.513
37 H25 H H25 N N N 0 5.562 1.296 -3.003
38 H26 H H26 N N N 0 6.487 2.167 0.268
39 H28 H H28 N N N 0 5.572 1.987 2.512
40 H29 H H29 N N N 0 6.099 0.286 2.504
41 H3 H H3 N N N 0 -4.585 0.904 1.72
42 H30 H H30 N N N 0 7.306 1.593 2.43
43 H31 H H31 N N N 0 4.952 -2.172 1.494
44 H32 H H32 N N N 0 1.911 -4.325 1.027
45 H33 H H33 N N N 0 1.982 -3.588 -0.463
46 H35 H H35 N N N 0 -2.919 -3.572 1.212
47 H36 H H36 N N N 0 -3.552 -2.036 1.129
48 H38 H H38 N N N 0 -1.916 3.246 1.099
49 H39 H H39 N N N 0 -3.334 3.543 1.917
50 H4 H H4 N N N 0 -3.78 2.953 -0.398
51 H41 H H41 N N N 0 -6.489 2.345 1.818
52 H42 H H42 N N N 0 -7.261 -0.228 -0.326
53 H5 H H5 N N N 0 -1.403 -1.904 2.166
54 H6 H H6 N N N 0 2.495 1.296 -1.045
55 H7 H H7 N N N 0 3.11 1.289 -2.716
56 H8 H H8 N N N 0 3.414 -2.174 -0.493
57 H9 H H9 N N N 0 -1.412 -0.963 -0.738
58 N23 N N4 N N N 0 -2.776 2.847 1.446
59 N25 N N3 N N N 0 -2.821 -2.653 0.808
60 N28 N N2 N N N 0 2.004 -3.448 0.536
61 N32 N N1 N N N 0 6.234 1.269 0.652
62 O03 O O7 N N N 0 5.666 0.979 -2.096
63 O05 O O6 N N N 0 3.268 -0.504 -1.701
64 O07 O O5 N N N 0 2.431 -0.635 0.474
65 O10 O O4 N N N 0 0.223 1.037 -0.081
66 O12 O O3 N N N 0 -2.33 0.149 0.742
67 O14 O O2 N N N 0 -3.457 0.439 -1.281
68 O17 O O1 N N N 0 -4.557 -1.943 -2.457
69 O19 O O10 N N N 0 -6.742 0.256 0.331
70 O21 O O9 N N N 0 -5.651 2.654 1.447
71 O30 O O8 N N N 0 4.994 -1.207 1.454



827 : Chemical Bonds

Total Number of Bonds: 73
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N28 C27 N C sing 1.47 N N
2 O30 C29 O C sing 1.43 N N
3 C27 C26 C C sing 1.53 N N
4 C27 C08 C C sing 1.53 N N
5 C26 C24 C C sing 1.53 N N
6 C29 C06 C C sing 1.53 N N
7 C29 C31 C C sing 1.53 N N
8 N32 C33 N C sing 1.47 N N
9 N32 C31 N C sing 1.47 N N
10 C06 O07 C O sing 1.43 N N
11 C06 O05 C O sing 1.43 N N
12 O07 C08 O C sing 1.43 N N
13 C24 N25 C N sing 1.47 N N
14 C24 C11 C C sing 1.53 N N
15 C08 C09 C C sing 1.53 N N
16 C31 C02 C C sing 1.53 N N
17 O05 C04 O C sing 1.43 N N
18 C09 C11 C C sing 1.53 N N
19 C09 O10 C O sing 1.43 N N
20 C11 O12 C O sing 1.43 N N
21 C02 O03 C O sing 1.43 N N
22 C02 C04 C C sing 1.53 N N
23 C02 C01 C C sing 1.53 N N
24 O12 C13 O C sing 1.43 N N
25 C16 C15 C C sing 1.53 N N
26 C16 O17 C O sing 1.43 N N
27 O14 C15 O C sing 1.43 N N
28 O14 C13 O C sing 1.43 N N
29 C15 C18 C C sing 1.53 N N
30 C13 C22 C C sing 1.53 N N
31 C18 C20 C C sing 1.53 N N
32 C18 O19 C O sing 1.43 N N
33 C22 C20 C C sing 1.53 N N
34 C22 N23 C N sing 1.47 N N
35 C20 O21 C O sing 1.43 N N
36 C13 H1 C H sing 1.09 N N
37 C15 H2 C H sing 1.09 N N
38 C20 H3 C H sing 1.09 N N
39 C22 H4 C H sing 1.09 N N
40 C24 H5 C H sing 1.09 N N
41 C04 H6 C H sing 1.09 N N
42 C04 H7 C H sing 1.09 N N
43 C06 H8 C H sing 1.09 N N
44 C11 H9 C H sing 1.09 N N
45 O17 H10 O H sing 0.97 N N
46 C18 H11 C H sing 1.09 N N
47 C27 H12 C H sing 1.09 N N
48 C09 H13 C H sing 1.09 N N
49 C31 H14 C H sing 1.09 N N
50 C01 H15 C H sing 1.09 N N
51 C01 H16 C H sing 1.09 N N
52 C01 H17 C H sing 1.09 N N
53 C16 H18 C H sing 1.09 N N
54 C16 H19 C H sing 1.09 N N
55 C26 H20 C H sing 1.09 N N
56 C26 H21 C H sing 1.09 N N
57 C08 H22 C H sing 1.09 N N
58 O10 H23 O H sing 0.97 N N
59 C29 H24 C H sing 1.09 N N
60 O03 H25 O H sing 0.97 N N
61 N32 H26 N H sing 1.01 N N
62 C33 H28 C H sing 1.09 N N
63 C33 H29 C H sing 1.09 N N
64 C33 H30 C H sing 1.09 N N
65 O30 H31 O H sing 0.97 N N
66 N28 H32 N H sing 1.01 N N
67 N28 H33 N H sing 1.01 N N
68 N25 H35 N H sing 1.01 N N
69 N25 H36 N H sing 1.01 N N
70 N23 H38 N H sing 1.01 N N
71 N23 H39 N H sing 1.01 N N
72 O21 H41 O H sing 0.97 N N
73 O19 H42 O H sing 0.97 N N



827 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
827 5u19 Open in New Window Bound ligand 1 1