Chemical Components in the PDB

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AKN : Summary

Code

AKN

One-letter code

X

Molecule name

(2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S ,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide

Synonyms

AMIKACIN

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-4-amino-N-{(1R,2S,3S,4R,5S)-5-amino-2-[(3-amino-3-deoxy-alpha-D-glucopyranosyl)oxy]-4-[(6-amino-6-deoxy-alpha-D-glucopyranosyl)oxy]-3-hydroxycyclohexyl}-2-hydroxybutanamide
OpenEye OEToolkits 1.9.2 (2S)-N-[(1R,2S,3S,4R,5S)-4-[(2R,3R,4S,5S,6R)-6-(aminomethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-5-azanyl-2-[(2S,3R,4S,5S,6R)-4-azanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]oxy-3-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide

Formula

C22 H43 N5 O13

Formal charge

0

Molecular weight

585.603 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC3C(OC1OC(C(O)C(N)C1O)CO)C(O)C(OC2OC(CN)C(O)C(O)C2O)C(N)C3)C(O)CCN
SMILES CACTVS 3.385 NCC[CH](O)C(=O)N[CH]1C[CH](N)[CH](O[CH]2O[CH](CN)[CH](O)[CH](O)[CH]2O)[CH](O)[CH]1O[CH]3O[CH](CO)[CH](O)[CH](N)[CH]3O
SMILES OpenEye OEToolkits 1.9.2 C1C(C(C(C(C1NC(=O)C(CCN)O)OC2C(C(C(C(O2)CO)O)N)O)O)OC3C(C(C(C(O3)CN)O)O)O)N
Canonical SMILES CACTVS 3.385 NCC[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)[C@@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@H]1O[C@H]3O[C@H](CO)[C@@H](O)[C@H](N)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.9.2 C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1NC(=O)[C@H](CCN)O)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@H]([C@@H]([C@H](O3)CN)O)O)O)N

IUPAC InChI

InChI=1S/C22H43N5O13/c23-2-1-8(29)20(36)27-7-3-6(25)18(39-22-16(34)15(33)13(31)9(4-24)37-22)17(35)19(7)40-21-14(32)11(26)12(30)10(5-28)38-21/h6-19,21-22,28-35H,1-5,23-26H2,(H,27,36)/t6-,7+,8-,9+,10+,11-,12+,13+,14+,15-,16+,17-,18+,19-,21+,22+/m0/s1

IUPAC InChI key

LKCWBDHBTVXHDL-RMDFUYIESA-N
AKN

wwPDB Information

Atom count

83 (40 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-02-28

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



AKN : Atoms of Molecule

Total Number of Atoms: 83
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 R N N 0 3.606 0.41 0.388
2 C3 C C2 R N N 0 4.838 1.068 -0.24
3 C4 C C3 S N N 0 5.69 -0.0070 -0.921
4 C5 C C4 S N N 0 6.064 -1.076 0.11
5 C7 C C5 R N N 0 4.786 -1.652 0.724
6 C9 C C6 N N N 0 5.152 -2.678 1.798
7 O6 O O1 N N N 0 6.799 -2.121 -0.531
8 O2 O O2 N N N 0 2.811 -0.188 -0.638
9 O8 O O3 N N N 0 4.025 -0.595 1.314
10 N10 N N1 N N N 0 3.929 -3.316 2.303
11 C11 C C7 R N N 0 -1.298 -1.195 -0.758
12 N12 N N2 N N N 0 -2.624 -1.626 -0.309
13 C13 C C8 N N N 0 -0.285 -2.312 -0.503
14 C14 C C9 S N N 0 1.1 -1.862 -0.972
15 N15 N N3 N N N 0 2.073 -2.935 -0.727
16 C16 C C10 R N N 0 1.518 -0.609 -0.2
17 C17 C C11 S N N 0 0.504 0.509 -0.456
18 O18 O O4 N N N 0 0.894 1.679 0.266
19 C19 C C12 S N N 0 -0.881 0.059 0.014
20 O20 O O5 N N N 0 -1.827 1.102 -0.225
21 C21 C C13 S N N 0 -2.348 1.698 0.965
22 C22 C C14 R N N 0 -3.717 2.317 0.669
23 O23 O O6 N N N 0 -4.595 1.311 0.159
24 C24 C C15 S N N 0 -3.551 3.428 -0.373
25 N25 N N4 N N N 0 -4.847 4.078 -0.607
26 C26 C C16 S N N 0 -2.548 4.459 0.152
27 O27 O O7 N N N 0 -2.331 5.463 -0.842
28 C28 C C17 R N N 0 -1.225 3.757 0.468
29 O29 O O8 N N N 0 -1.454 2.716 1.419
30 C30 C C18 N N N 0 -0.236 4.77 1.049
31 O31 O O9 N N N 0 1.031 4.14 1.246
32 O32 O O10 N N N 0 4.423 2.033 -1.208
33 O33 O O11 N N N 0 6.878 0.588 -1.448
34 N37 N N5 N N N 0 -5.865 -5.062 2.172
35 C35 C C19 N N N 0 -3.411 -2.35 -1.129
36 O36 O O12 N N N 0 -3.021 -2.645 -2.239
37 C37 C C20 S N N 0 -4.775 -2.794 -0.667
38 C38 C C21 N N N 0 -4.626 -3.77 0.501
39 C39 C C22 N N N 0 -6.009 -4.124 1.05
40 O40 O O13 N N N 0 -5.456 -3.44 -1.745
41 H1 H H1 N N N 0 3.018 1.163 0.911
42 H2 H H2 N N N 0 5.423 1.56 0.537
43 H3 H H3 N N N 0 5.122 -0.464 -1.731
44 H4 H H4 N N N 0 6.675 -0.628 0.894
45 H5 H H5 N N N 0 4.194 -2.135 -0.054
46 H6 H H6 N N N 0 5.807 -3.436 1.368
47 H7 H H7 N N N 0 5.665 -2.177 2.619
48 H8 H H8 N N N 0 7.623 -1.827 -0.942
49 H9 H H9 N N N 0 3.401 -3.733 1.55
50 H10 H H10 N N N 0 4.144 -3.999 3.014
51 H12 H H12 N N N 0 -1.331 -0.971 -1.825
52 H13 H H13 N N N 0 -2.936 -1.39 0.578
53 H14 H H14 N N N 0 -0.252 -2.536 0.563
54 H15 H H15 N N N 0 -0.582 -3.205 -1.053
55 H16 H H16 N N N 0 1.067 -1.638 -2.038
56 H17 H H17 N N N 0 1.727 -3.821 -1.064
57 H18 H H18 N N N 0 2.966 -2.715 -1.14
58 H20 H H20 N N N 0 1.55 -0.833 0.866
59 H21 H H21 N N N 0 0.472 0.733 -1.522
60 H22 H H22 N N N 0 1.688 2.109 -0.082
61 H23 H H23 N N N 0 -0.848 -0.166 1.08
62 H24 H H24 N N N 0 -2.453 0.935 1.737
63 H25 H H25 N N N 0 -4.133 2.735 1.585
64 H26 H H26 N N N 0 -4.742 0.573 0.766
65 H27 H H27 N N N 0 -3.183 3.001 -1.306
66 H28 H H28 N N N 0 -5.528 3.415 -0.947
67 H29 H H29 N N N 0 -5.177 4.539 0.227
68 H31 H H31 N N N 0 -2.941 4.922 1.057
69 H32 H H32 N N N 0 -1.705 6.15 -0.576
70 H33 H H33 N N N 0 -0.812 3.331 -0.446
71 H34 H H34 N N N 0 -0.123 5.606 0.358
72 H35 H H35 N N N 0 -0.611 5.137 2.005
73 H36 H H36 N N N 0 1.709 4.725 1.613
74 H37 H H37 N N N 0 3.874 2.742 -0.846
75 H38 H H38 N N N 0 6.714 1.279 -2.104
76 H39 H H39 N N N 0 -5.263 -4.681 2.886
77 H40 H H40 N N N 0 -6.766 -5.311 2.553
78 H42 H H42 N N N 0 -5.349 -1.925 -0.343
79 H43 H H43 N N N 0 -4.129 -4.677 0.155
80 H44 H H44 N N N 0 -4.029 -3.308 1.287
81 H45 H H45 N N N 0 -6.605 -4.587 0.264
82 H46 H H46 N N N 0 -6.505 -3.217 1.396
83 H47 H H47 N N N 0 -5.001 -4.223 -2.084



AKN : Chemical Bonds

Total Number of Bonds: 85
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C5 O C sing 1.43 N N
2 C9 C7 C C sing 1.53 N N
3 C9 N10 C N sing 1.47 N N
4 C5 C7 C C sing 1.53 N N
5 C5 C4 C C sing 1.53 N N
6 O33 C4 O C sing 1.43 N N
7 C7 O8 C O sing 1.43 N N
8 N15 C14 N C sing 1.47 N N
9 C4 C3 C C sing 1.53 N N
10 C14 C13 C C sing 1.53 N N
11 C14 C16 C C sing 1.53 N N
12 O8 C1 O C sing 1.43 N N
13 O2 C1 O C sing 1.43 N N
14 O2 C16 O C sing 1.43 N N
15 C3 C1 C C sing 1.53 N N
16 C3 O32 C O sing 1.43 N N
17 C13 C11 C C sing 1.53 N N
18 C16 C17 C C sing 1.53 N N
19 O36 C35 O C doub 1.21 N N
20 C11 N12 C N sing 1.46 N N
21 C11 C19 C C sing 1.53 N N
22 C35 N12 C N sing 1.35 N N
23 C35 C37 C C sing 1.51 N N
24 C17 C19 C C sing 1.53 N N
25 C17 O18 C O sing 1.43 N N
26 C37 O40 C O sing 1.43 N N
27 C37 C38 C C sing 1.53 N N
28 C19 O20 C O sing 1.43 N N
29 C38 C39 C C sing 1.53 N N
30 C39 N37 C N sing 1.47 N N
31 O20 C21 O C sing 1.43 N N
32 O23 C22 O C sing 1.43 N N
33 C21 C22 C C sing 1.53 N N
34 C21 O29 C O sing 1.43 N N
35 C22 C24 C C sing 1.53 N N
36 O29 C28 O C sing 1.43 N N
37 C24 N25 C N sing 1.47 N N
38 C24 C26 C C sing 1.53 N N
39 C28 C26 C C sing 1.53 N N
40 C28 C30 C C sing 1.53 N N
41 C26 O27 C O sing 1.43 N N
42 C30 O31 C O sing 1.43 N N
43 C1 H1 C H sing 1.09 N N
44 C3 H2 C H sing 1.09 N N
45 C4 H3 C H sing 1.09 N N
46 C5 H4 C H sing 1.09 N N
47 C7 H5 C H sing 1.09 N N
48 C9 H6 C H sing 1.09 N N
49 C9 H7 C H sing 1.09 N N
50 O6 H8 O H sing 0.97 N N
51 N10 H9 N H sing 1.01 N N
52 N10 H10 N H sing 1.01 N N
53 C11 H12 C H sing 1.09 N N
54 N12 H13 N H sing 0.97 N N
55 C13 H14 C H sing 1.09 N N
56 C13 H15 C H sing 1.09 N N
57 C14 H16 C H sing 1.09 N N
58 N15 H17 N H sing 1.01 N N
59 N15 H18 N H sing 1.01 N N
60 C16 H20 C H sing 1.09 N N
61 C17 H21 C H sing 1.09 N N
62 O18 H22 O H sing 0.97 N N
63 C19 H23 C H sing 1.09 N N
64 C21 H24 C H sing 1.09 N N
65 C22 H25 C H sing 1.09 N N
66 O23 H26 O H sing 0.97 N N
67 C24 H27 C H sing 1.09 N N
68 N25 H28 N H sing 1.01 N N
69 N25 H29 N H sing 1.01 N N
70 C26 H31 C H sing 1.09 N N
71 O27 H32 O H sing 0.97 N N
72 C28 H33 C H sing 1.09 N N
73 C30 H34 C H sing 1.09 N N
74 C30 H35 C H sing 1.09 N N
75 O31 H36 O H sing 0.97 N N
76 O32 H37 O H sing 0.97 N N
77 O33 H38 O H sing 0.97 N N
78 N37 H39 N H sing 1.01 N N
79 N37 H40 N H sing 1.01 N N
80 C37 H42 C H sing 1.09 N N
81 C38 H43 C H sing 1.09 N N
82 C38 H44 C H sing 1.09 N N
83 C39 H45 C H sing 1.09 N N
84 C39 H46 C H sing 1.09 N N
85 O40 H47 O H sing 0.97 N N



AKN : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
AKN 4p20 Open in New Window Bound ligand 2 1
AKN 6cgd Open in New Window Bound ligand 2 1
AKN 6ypu Open in New Window Bound ligand 1 1