Chemical Components in the PDB

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JS4 : Summary

Code

JS4

One-letter code

X

Molecule name

(2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3R,4R,5S)-4-(2-(3-AMINOPROPYLAMINO)ETHOXY)-5-((1R,2R,3S,5R,6S)-3,5-DIAM INO-2-((2S,3R,4R,5S,6R)-3-AMINO-4,5-DIHYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-2-( HYDROXYMETHYL)-TETRAHYDROFURAN-3-YLOXY)-TETRAHYDRO-2H-PYRAN-3,4-DIOL

Systematic names

ProgramVersionName
ACDLabs 10.04 (1R,2R,3S,4R,6S)-4,6-diamino-2-{[2-O-{2-[(3-aminopropyl)amino]ethyl}-3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside
OpenEye OEToolkits 1.5.0 (2R,3S,4R,5R,6S)-5-amino-6-[(1R,2R,3S,4R,6S)-4,6-diamino-2-[(2S,3R,5R)-4-[(2R,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxy-oxan-2-yl]oxy-3-[2-(3-aminopropylamino)ethoxy]-5-(hydroxymethyl)oxolan-2-yl]oxy-3-hydroxy-cyclohexyl]oxy-2-(hydroxymethyl)oxane-3,4-diol

Formula

C28 H57 N7 O14

Formal charge

0

Molecular weight

715.791 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O(C2C(OC1OC(CO)C(O)C(O)C1N)C(N)CC(N)C2O)C4OC(C(OC3OC(CN)C(O)C(O)C3N)C4OCCNCCCN)CO
SMILES CACTVS 3.341 NCCCNCCO[CH]1[CH](O[CH](CO)[CH]1O[CH]2O[CH](CN)[CH](O)[CH](O)[CH]2N)O[CH]3[CH](O)[CH](N)C[CH](N)[CH]3O[CH]4O[CH](CO)[CH](O)[CH](O)[CH]4N
SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(C(C1N)OC2C(C(C(C(O2)CO)O)O)N)OC3C(C(C(O3)CO)OC4C(C(C(C(O4)CN)O)O)N)OCCNCCCN)O)N
Canonical SMILES CACTVS 3.341 NCCCNCCO[C@H]1[C@@H](O[C@H](CO)[C@H]1O[C@H]2O[C@@H](CN)[C@@H](O)[C@H](O)[C@H]2N)O[C@@H]3[C@@H](O)[C@H](N)C[C@H](N)[C@H]3O[C@H]4O[C@H](CO)[C@@H](O)[C@H](O)[C@H]4N
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)O)N)O[C@H]3[C@@H](C([C@H](O3)CO)O[C@@H]4[C@@H]([C@H]([C@@H]([C@@H](O4)CN)O)O)N)OCCNCCCN)O)N

IUPAC InChI

InChI=1S/C28H57N7O14/c29-2-1-3-35-4-5-43-25-23(48-26-15(33)20(41)18(39)12(7-30)44-26)14(9-37)46-28(25)49-24-17(38)10(31)6-11(32)22(24)47-27-16(34)21(42)19(40)13(8-36)45-27/h10-28,35-42H,1-9,29-34H2/t10-,11+,12+,13-,14-,15-,16-,17+,18-,19-,20-,21-,22-,23-,24-,25-,26-,27-,28+/m1/s1

IUPAC InChI key

FJVLHNJZMYGVLT-XXJRHLBLSA-N
JS4

wwPDB Information

Atom count

106 (49 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-11-16

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



JS4 : Atoms of Molecule

Total Number of Atoms: 106
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 3.331 0.955 0.89
2 O11 O O11 N N N 0 3.703 0.519 -0.419
3 C21 C C21 R N N 0 3.094 2.467 0.876
4 N21 N N21 N N N 0 1.998 2.783 -0.05
5 C31 C C31 R N N 0 4.374 3.17 0.414
6 O31 O O31 N N N 0 4.219 4.585 0.537
7 C41 C C41 S N N 0 5.536 2.701 1.298
8 O41 O O41 N N N 0 6.765 3.229 0.794
9 C51 C C51 R N N 0 5.59 1.172 1.281
10 O51 O O51 N N N 0 4.376 0.64 1.809
11 C61 C C61 N N N 0 6.767 0.696 2.134
12 O61 O O61 N N N 0 6.884 -0.724 2.035
13 C12 C C12 R N N 0 3.094 -3.412 -1.865
14 N12 N N12 N N N 0 2.972 -4.876 -1.876
15 C22 C C22 N N N 0 4.497 -3.021 -1.395
16 C32 C C32 S N N 0 4.624 -1.496 -1.383
17 N32 N N32 N N N 0 5.971 -1.12 -0.932
18 C42 C C42 R N N 0 3.584 -0.905 -0.43
19 C52 C C52 R N N 0 2.181 -1.296 -0.9
20 O52 O O52 N N N 0 1.209 -0.743 -0.01
21 C62 C C62 S N N 0 2.054 -2.82 -0.911
22 O62 O O62 N N N 0 0.744 -3.186 -1.35
23 C13 C C13 S N N 0 0.032 -0.501 -0.782
24 C23 C C23 R N N 0 -1.119 -0.017 0.128
25 O23 O O23 N N N 0 -1.99 -1.102 0.453
26 C33 C C33 R N N 0 -1.86 1.035 -0.726
27 C43 C C43 R N N 0 -1.068 1.061 -2.056
28 O43 O O43 N N N 0 0.251 0.585 -1.709
29 C53 C C53 N N N 0 -0.993 2.487 -2.604
30 O33 O O33 N N N 0 -3.212 0.635 -0.956
31 O53 O O53 N N N 0 -0.273 2.485 -3.839
32 C63 C C63 N N N 0 -1.53 -1.644 1.693
33 C73 C C73 N N N 0 -2.425 -2.817 2.1
34 N73 N N73 N N N 0 -2.282 -3.905 1.123
35 C83 C C83 N N N 0 -3.162 -4.992 1.57
36 C15 C C15 N N N 0 -3.061 -6.165 0.592
37 C25 C C25 N N N 0 -3.978 -7.298 1.058
38 N25 N N25 N N N 0 -3.881 -8.423 0.119
39 C14 C C14 R N N 0 -4.02 1.349 -0.018
40 C24 C C24 R N N 0 -5.428 0.75 0.0
41 N24 N N24 N N N 0 -6.041 0.886 -1.328
42 C34 C C34 R N N 0 -6.276 1.499 1.035
43 O34 O O34 N N N 0 -5.766 1.255 2.347
44 C44 C C44 S N N 0 -6.209 3.0 0.728
45 O44 O O44 N N N 0 -6.848 3.263 -0.523
46 C54 C C54 S N N 0 -4.742 3.429 0.654
47 O54 O O54 N N N 0 -4.085 2.722 -0.396
48 C64 C C64 N N N 0 -4.667 4.932 0.381
49 N64 N N64 N N N 0 -3.259 5.348 0.316
50 H11 H H11 N N N 0 2.416 0.447 1.195
51 H21 H H21 N N N 0 2.834 2.805 1.879
52 H211 H 1H21 N N N 0 1.181 2.301 0.293
53 H212 H 2H21 N N N 0 1.814 3.771 0.046
54 H31 H H31 N N N 0 4.578 2.913 -0.625
55 H5 H H5 N N N 0 5.051 4.984 0.248
56 H41 H H41 N N N 0 5.381 3.05 2.319
57 H4 H H4 N N N 0 7.467 2.904 1.374
58 H51 H H51 N N N 0 5.722 0.825 0.256
59 H611 H 1H61 N N N 0 7.686 1.162 1.777
60 H612 H 2H61 N N N 0 6.598 0.975 3.174
61 H61 H H61 N N N 0 7.636 -0.982 2.586
62 H12 H H12 N N N 0 2.927 -3.026 -2.87
63 H121 H 1H12 N N N 0 3.674 -5.22 -2.514
64 H122 H 2H12 N N N 0 3.235 -5.196 -0.956
65 H321 H 1H32 N N N 0 6.623 -1.627 -1.512
66 H221 H 1H22 N N N 0 4.664 -3.407 -0.389
67 H222 H 2H22 N N N 0 5.238 -3.442 -2.074
68 H32 H H32 N N N 0 4.457 -1.11 -2.389
69 H322 H 2H32 N N N 0 6.087 -0.142 -1.15
70 H42 H H42 N N N 0 3.751 -1.291 0.576
71 H52 H H52 N N N 0 2.014 -0.91 -1.905
72 H62 H H62 N N N 0 2.221 -3.207 0.094
73 H3 H H3 N N N 0 0.706 -4.152 -1.343
74 H13 H H13 N N N 0 -0.262 -1.404 -1.318
75 H23 H H23 N N N 0 -0.722 0.437 1.036
76 H33 H H33 N N N 0 -1.829 2.013 -0.244
77 H43 H H43 N N N 0 -1.531 0.398 -2.787
78 H531 H 1H53 N N N 0 -2.001 2.865 -2.772
79 H532 H 2H53 N N N 0 -0.48 3.126 -1.886
80 H53 H H53 N N N 0 -0.248 3.4 -4.15
81 H631 H 1H63 N N N 0 -1.569 -0.874 2.463
82 H632 H 2H63 N N N 0 -0.504 -1.993 1.579
83 H731 H 1H73 N N N 0 -3.464 -2.488 2.128
84 H732 H 2H73 N N N 0 -2.13 -3.173 3.087
85 H73 H H73 N N N 0 -1.335 -4.245 1.205
86 H831 H 1H83 N N N 0 -4.191 -4.636 1.605
87 H832 H 2H83 N N N 0 -2.858 -5.321 2.564
88 H151 H 1H15 N N N 0 -2.032 -6.521 0.558
89 H152 H 2H15 N N N 0 -3.365 -5.836 -0.401
90 H11A H 1H1 N N N 0 -5.007 -6.941 1.093
91 H12A H 2H1 N N N 0 -3.673 -7.626 2.052
92 H251 H 1H25 N N N 0 -2.942 -8.785 0.197
93 H252 H 2H25 N N N 0 -4.499 -9.143 0.465
94 H14 H H14 N N N 0 -3.579 1.267 0.976
95 H24 H H24 N N N 0 -5.372 -0.304 0.27
96 H241 H 1H24 N N N 0 -5.452 0.38 -1.972
97 H242 H 2H24 N N N 0 -6.921 0.394 -1.293
98 H34 H H34 N N N 0 -7.31 1.159 0.975
99 H2 H H2 N N N 0 -6.321 1.755 2.961
100 H44 H H44 N N N 0 -6.713 3.556 1.519
101 H1 H H1 N N N 0 -7.768 2.978 -0.432
102 H54 H H54 N N N 0 -4.252 3.208 1.602
103 H641 H 1H64 N N N 0 -5.155 5.154 -0.568
104 H642 H 2H64 N N N 0 -5.169 5.473 1.183
105 H21A H 1H2 N N N 0 -3.258 6.341 0.135
106 H22 H 2H2 N N N 0 -2.877 5.222 1.241



JS4 : Chemical Bonds

Total Number of Bonds: 109
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 H211 N H sing 1.01 N N
10 N21 H212 N H sing 1.01 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 1.09 N N
14 O31 H5 O H sing 0.97 N N
15 C41 O41 C O sing 1.43 N N
16 C41 C51 C C sing 1.53 N N
17 C41 H41 C H sing 1.09 N N
18 O41 H4 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 1.09 N N
22 C61 O61 C O sing 1.43 N N
23 C61 H611 C H sing 1.09 N N
24 C61 H612 C H sing 1.09 N N
25 O61 H61 O H sing 0.97 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 H121 N H sing 1.01 N N
31 N12 H122 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 H321 N H sing 1.01 N N
39 N32 H322 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 C13 O C sing 1.43 N N
46 C62 O62 C O sing 1.43 N N
47 C62 H62 C H sing 1.09 N N
48 O62 H3 O H sing 0.97 N N
49 C13 C23 C C sing 1.55 N N
50 C13 O43 C O sing 1.44 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 1.54 N N
54 C23 H23 C H sing 1.09 N N
55 O23 C63 O C sing 1.43 N N
56 C33 C43 C C sing 1.55 N N
57 C33 O33 C O sing 1.43 N N
58 C33 H33 C H sing 1.09 N N
59 C43 O43 C O sing 1.44 N N
60 C43 C53 C C sing 1.53 N N
61 C43 H43 C H sing 1.09 N N
62 C53 O53 C O sing 1.43 N N
63 C53 H531 C H sing 1.09 N N
64 C53 H532 C H sing 1.09 N N
65 O33 C14 O C sing 1.43 N N
66 O53 H53 O H sing 0.97 N N
67 C63 C73 C C sing 1.53 N N
68 C63 H631 C H sing 1.09 N N
69 C63 H632 C H sing 1.09 N N
70 C73 N73 C N sing 1.47 N N
71 C73 H731 C H sing 1.09 N N
72 C73 H732 C H sing 1.09 N N
73 N73 C83 N C sing 1.47 N N
74 N73 H73 N H sing 1.01 N N
75 C83 C15 C C sing 1.53 N N
76 C83 H831 C H sing 1.09 N N
77 C83 H832 C H sing 1.09 N N
78 C15 C25 C C sing 1.53 N N
79 C15 H151 C H sing 1.09 N N
80 C15 H152 C H sing 1.09 N N
81 C25 N25 C N sing 1.47 N N
82 C25 H11A C H sing 1.09 N N
83 C25 H12A C H sing 1.09 N N
84 N25 H251 N H sing 1.01 N N
85 N25 H252 N H sing 1.01 N N
86 C14 C24 C C sing 1.53 N N
87 C14 O54 C O sing 1.43 N N
88 C14 H14 C H sing 1.09 N N
89 C24 N24 C N sing 1.47 N N
90 C24 C34 C C sing 1.53 N N
91 C24 H24 C H sing 1.09 N N
92 N24 H241 N H sing 1.01 N N
93 N24 H242 N H sing 1.01 N N
94 C34 O34 C O sing 1.43 N N
95 C34 C44 C C sing 1.53 N N
96 C34 H34 C H sing 1.09 N N
97 O34 H2 O H sing 0.97 N N
98 C44 O44 C O sing 1.43 N N
99 C44 C54 C C sing 1.53 N N
100 C44 H44 C H sing 1.09 N N
101 O44 H1 O H sing 0.97 N N
102 C54 O54 C O sing 1.43 N N
103 C54 C64 C C sing 1.53 N N
104 C54 H54 C H sing 1.09 N N
105 C64 N64 C N sing 1.47 N N
106 C64 H641 C H sing 1.09 N N
107 C64 H642 C H sing 1.09 N N
108 N64 H21A N H sing 1.01 N N
109 N64 H22 N H sing 1.01 N N



JS4 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
JS4 2bee Open in New Window Bound ligand 2 1