Chemical Components in the PDB

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LIV : Summary

Code

LIV

One-letter code

X

Molecule name

(2R,3S,4S,5S,6R)-2-((2S,3S,4R,5R,6R)-5-AMINO-2-(AMINOMETHYL)-6-((2R,3S,4R,5S)-5-((1R,2R,3S,5R,6S)-3,5-DIAMINO-2-((2S,3R ,5S,6R)-3-AMINO-5-HYDROXY-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-2-YLOXY)-6-HYDROXYCYCLOHEXYLOXY)-4-HYDROXY-2-(HYDROXYMET HYL)-TETRAHYDROFURAN-3-YLOXY)-4-HYDROXY-TETRAHYDRO-2H-PYRAN-3-YLOXY)-6-(HYDROXYMETHYL)-TETRAHYDRO-2H-PYRAN-3,4,5-TRIOL

Systematic names

ProgramVersionName
ACDLabs 10.04 (1R,2R,3S,4R,6S)-4,6-diamino-3-hydroxy-2-{[alpha-D-mannopyranosyl-(1->4)-2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl-(1->3)-beta-D-ribofuranosyl]oxy}cyclohexyl 2-amino-2,3-dideoxy-alpha-D-ribo-hexopyranoside
OpenEye OEToolkits 1.5.0 (2R,3S,4S,5S,6R)-2-[(2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(2R,3S,4R,5S)-5-[(1R,2R,3S,5R,6S)-3,5-diamino-2-[(2S,3R,5S,6R)-3-amino-5-hydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxy-cyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxy-4-hydroxy-oxan-3-yl]oxy-6-(hydroxymethyl)oxane-3,4,5-triol

Formula

C29 H55 N5 O18

Formal charge

0

Molecular weight

761.77 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O(C2C(OC1OC(CO)C(O)CC1N)C(N)CC(N)C2O)C5OC(C(OC4OC(CN)C(OC3OC(CO)C(O)C(O)C3O)C(O)C4N)C5O)CO
SMILES CACTVS 3.341 NC[CH]1O[CH](O[CH]2[CH](O)[CH](O[CH]2CO)O[CH]3[CH](O)[CH](N)C[CH](N)[CH]3O[CH]4O[CH](CO)[CH](O)C[CH]4N)[CH](N)[CH](O)[CH]1O[CH]5O[CH](CO)[CH](O)[CH](O)[CH]5O
SMILES OpenEye OEToolkits 1.5.0 C1C(C(C(C(C1N)OC2C(CC(C(O2)CO)O)N)OC3C(C(C(O3)CO)OC4C(C(C(C(O4)CN)OC5C(C(C(C(O5)CO)O)O)O)O)N)O)O)N
Canonical SMILES CACTVS 3.341 NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO)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[C@H]4N)[C@H](N)[C@@H](O)[C@@H]1O[C@H]5O[C@H](CO)[C@@H](O)[C@H](O)[C@@H]5O
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[C@@H]([C@H](O2)CO)O)N)O[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O[C@@H]4[C@@H]([C@H]([C@@H]([C@@H](O4)CN)O[C@@H]5[C@H]([C@H]([C@@H]([C@H](O5)CO)O)O)O)O)N)O)O)N

IUPAC InChI

InChI=1S/C29H55N5O18/c30-3-11-23(51-28-20(43)19(42)17(40)13(5-36)47-28)18(41)15(34)27(45-11)50-24-14(6-37)48-29(21(24)44)52-25-16(39)7(31)1-8(32)22(25)49-26-9(33)2-10(38)12(4-35)46-26/h7-29,35-44H,1-6,30-34H2/t7-,8+,9-,10+,11+,12-,13-,14-,15-,16+,17-,18-,19+,20+,21-,22-,23-,24-,25-,26-,27-,28-,29+/m1/s1

IUPAC InChI key

DBLVDAUGBTYDFR-SWMBIRFSSA-N
LIV

wwPDB Information

Atom count

107 (52 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAD

Is modified

No

Standard parent

Not Assigned

Defined at

2005-11-16

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



LIV : Atoms of Molecule

Total Number of Atoms: 107
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 -4.807 1.406 -0.569
2 O11 O O11 N N N 0 -5.277 0.67 0.563
3 C21 C C21 R N N 0 -4.021 2.629 -0.091
4 N21 N N21 N N N 0 -2.861 2.191 0.696
5 C31 C C31 N N N 0 -4.932 3.499 0.781
6 C41 C C41 S N N 0 -6.209 3.813 -0.006
7 O41 O O41 N N N 0 -7.137 4.498 0.837
8 C51 C C51 R N N 0 -6.831 2.501 -0.491
9 O51 O O51 N N N 0 -5.92 1.826 -1.356
10 C61 C C61 N N N 0 -8.124 2.803 -1.25
11 C62 C C62 S N N 0 -4.921 -2.964 -0.322
12 O61 O O61 N N N 0 -8.759 1.576 -1.615
13 C12 C C12 R N N 0 -6.089 -3.483 0.519
14 N12 N N12 N N N 0 -6.497 -4.806 0.027
15 O62 O O62 N N N 0 -3.821 -3.87 -0.221
16 C52 C C52 R N N 0 -4.496 -1.587 0.191
17 O52 O O52 N N N 0 -3.405 -1.101 -0.595
18 C42 C C42 R N N 0 -5.674 -0.616 0.083
19 C32 C C32 S N N 0 -6.841 -1.136 0.925
20 N32 N N32 N N N 0 -7.972 -0.204 0.821
21 C22 C C22 N N N 0 -7.266 -2.513 0.411
22 C33 C C33 S N N 0 0.106 -0.814 0.227
23 C13 C C13 S N N 0 -2.207 -1.554 0.038
24 C23 C C23 R N N 0 -0.974 -1.18 -0.815
25 O23 O O23 N N N 0 -0.551 -2.294 -1.604
26 C43 C C43 R N N 0 -0.599 -1.008 1.588
27 O43 O O43 N N N 0 -2.008 -0.869 1.294
28 C53 C C53 N N N 0 -0.155 0.065 2.584
29 O53 O O53 N N N 0 -0.788 -0.163 3.844
30 C44 C C44 S N N 0 4.736 -0.061 -1.445
31 O44 O O44 N N N 0 5.512 -0.355 -0.282
32 C34 C C34 R N N 0 4.253 -1.369 -2.083
33 O34 O O34 N N N 0 3.598 -1.09 -3.322
34 C24 C C24 R N N 0 3.271 -2.049 -1.123
35 N24 N N24 N N N 0 3.98 -2.467 0.094
36 C14 C C14 R N N 0 2.165 -1.056 -0.756
37 O33 O O33 N N N 0 1.228 -1.692 0.115
38 C54 C C54 S N N 0 3.519 0.781 -1.055
39 O54 O O54 N N N 0 2.731 0.076 -0.098
40 C64 C C64 N N N 0 3.99 2.105 -0.449
41 N64 N N64 N N N 0 2.831 2.974 -0.21
42 C15 C C15 R N N 0 6.834 -0.655 -0.732
43 C25 C C25 S N N 0 7.625 -1.304 0.407
44 C35 C C35 S N N 0 7.664 -0.344 1.6
45 C45 C C45 S N N 0 8.202 1.009 1.122
46 C55 C C55 R N N 0 7.369 1.484 -0.07
47 C65 C C65 N N N 0 7.879 2.851 -0.533
48 O25 O O25 N N N 0 8.957 -1.579 -0.03
49 O35 O O35 N N N 0 8.521 -0.87 2.614
50 O45 O O45 N N N 0 8.11 1.963 2.181
51 O55 O O55 N N N 0 7.48 0.549 -1.142
52 O65 O O65 N N N 0 7.027 3.353 -1.564
53 H11 H H11 N N N 0 -4.157 0.77 -1.17
54 H21 H H21 N N N 0 -3.682 3.204 -0.952
55 H211 H 1H21 N N N 0 -2.38 3.026 0.993
56 H212 H 2H21 N N N 0 -3.224 1.753 1.529
57 H311 H 1H31 N N N 0 -4.419 4.428 1.032
58 H312 H 2H31 N N N 0 -5.187 2.962 1.694
59 H41 H H41 N N N 0 -5.964 4.439 -0.864
60 H3 H H3 N N N 0 -6.706 5.317 1.12
61 H51 H H51 N N N 0 -7.053 1.867 0.367
62 H611 H 1H61 N N N 0 -8.793 3.382 -0.613
63 H612 H 2H61 N N N 0 -7.893 3.374 -2.149
64 H61 H H61 N N N 0 -9.569 1.811 -2.09
65 H12 H H12 N N N 0 -5.778 -3.564 1.561
66 H121 H 1H12 N N N 0 -7.265 -5.107 0.608
67 H122 H 2H12 N N N 0 -6.871 -4.667 -0.9
68 H62 H H62 N N N 0 -5.231 -2.883 -1.364
69 H2 H H2 N N N 0 -4.131 -4.724 -0.554
70 H52 H H52 N N N 0 -4.186 -1.667 1.233
71 H42 H H42 N N N 0 -5.984 -0.536 -0.958
72 H32 H H32 N N N 0 -6.531 -1.216 1.966
73 H321 H 1H32 N N N 0 -8.752 -0.642 1.288
74 H322 H 2H32 N N N 0 -7.728 0.61 1.365
75 H221 H 1H22 N N N 0 -7.577 -2.433 -0.63
76 H222 H 2H22 N N N 0 -8.098 -2.883 1.011
77 H13 H H13 N N N 0 -2.246 -2.632 0.196
78 H23 H H23 N N N 0 -1.196 -0.324 -1.452
79 H1 H H1 N N N 0 -1.262 -2.476 -2.234
80 H33 H H33 N N N 0 0.42 0.222 0.104
81 H43 H H43 N N N 0 -0.39 -2.001 1.984
82 H531 H 1H53 N N N 0 0.928 0.021 2.708
83 H532 H 2H53 N N N 0 -0.437 1.049 2.208
84 H53 H H53 N N N 0 -0.481 0.533 4.441
85 H44 H H44 N N N 0 5.345 0.49 -2.16
86 H34 H H34 N N N 0 5.105 -2.026 -2.26
87 H4 H H4 N N N 0 3.302 -1.939 -3.679
88 H24 H H24 N N N 0 2.832 -2.921 -1.607
89 H241 H 1H24 N N N 0 3.294 -2.9 0.694
90 H242 H 2H24 N N N 0 4.624 -3.193 -0.181
91 H14 H H14 N N N 0 1.655 -0.731 -1.662
92 H54 H H54 N N N 0 2.918 0.982 -1.942
93 H11A H 1H1 N N N 0 4.677 2.596 -1.139
94 H12A H 2H1 N N N 0 4.5 1.911 0.495
95 H641 H 1H64 N N N 0 3.187 3.831 0.187
96 H642 H 2H64 N N N 0 2.454 3.21 -1.116
97 H15 H H15 N N N 0 6.782 -1.343 -1.576
98 H25 H H25 N N N 0 7.138 -2.234 0.702
99 H35 H H35 N N N 0 6.658 -0.217 2.0
100 H45 H H45 N N N 0 9.244 0.901 0.819
101 H55 H H55 N N N 0 6.324 1.57 0.229
102 H651 H 1H65 N N N 0 7.877 3.543 0.309
103 H652 H 2H65 N N N 0 8.893 2.749 -0.918
104 H7 H H7 N N N 0 8.886 -2.185 -0.78
105 H6 H H6 N N N 0 8.146 -1.719 2.885
106 H5 H H5 N N N 0 8.648 1.625 2.91
107 H65 H H65 N N N 0 7.382 4.213 -1.827



LIV : Chemical Bonds

Total Number of Bonds: 111
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 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 H3 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 O61 C O sing 1.43 N N
22 C61 H611 C H sing 1.09 N N
23 C61 H612 C H sing 1.09 N N
24 O61 H61 O H sing 0.97 N N
25 C12 N12 C N sing 1.47 N N
26 C12 C62 C C sing 1.53 N N
27 C12 C22 C C sing 1.53 N N
28 C12 H12 C H sing 1.09 N N
29 N12 H121 N H sing 1.01 N N
30 N12 H122 N H sing 1.01 N N
31 C62 O62 C O sing 1.43 N N
32 C62 C52 C C sing 1.53 N N
33 C62 H62 C H sing 1.09 N N
34 O62 H2 O H sing 0.97 N N
35 C52 O52 C O sing 1.43 N N
36 C52 C42 C C sing 1.53 N N
37 C52 H52 C H sing 1.09 N N
38 O52 C13 O C sing 1.43 N N
39 C42 C32 C C sing 1.53 N N
40 C42 H42 C H sing 1.09 N N
41 C32 N32 C N sing 1.47 N N
42 C32 C22 C C sing 1.53 N N
43 C32 H32 C H sing 1.09 N N
44 N32 H321 N H sing 1.01 N N
45 N32 H322 N H sing 1.01 N N
46 C22 H221 C H sing 1.09 N N
47 C22 H222 C H sing 1.09 N N
48 C13 C23 C C sing 1.55 N N
49 C13 O43 C O sing 1.44 N N
50 C13 H13 C H sing 1.09 N N
51 C23 O23 C O sing 1.43 N N
52 C23 C33 C C sing 1.54 N N
53 C23 H23 C H sing 1.09 N N
54 O23 H1 O H sing 0.97 N N
55 C33 C43 C C sing 1.54 N N
56 C33 O33 C O sing 1.43 N N
57 C33 H33 C H sing 1.09 N N
58 C43 O43 C O sing 1.45 N N
59 C43 C53 C C sing 1.53 N N
60 C43 H43 C H sing 1.09 N N
61 C53 O53 C O sing 1.43 N N
62 C53 H531 C H sing 1.09 N N
63 C53 H532 C H sing 1.09 N N
64 O53 H53 O H sing 0.97 N N
65 C44 O44 C O sing 1.43 N N
66 C44 C34 C C sing 1.53 N N
67 C44 C54 C C sing 1.53 N N
68 C44 H44 C H sing 1.09 N N
69 O44 C15 O C sing 1.43 N N
70 C34 O34 C O sing 1.43 N N
71 C34 C24 C C sing 1.53 N N
72 C34 H34 C H sing 1.09 N N
73 O34 H4 O H sing 0.97 N N
74 C24 N24 C N sing 1.47 N N
75 C24 C14 C C sing 1.53 N N
76 C24 H24 C H sing 1.09 N N
77 N24 H241 N H sing 1.01 N N
78 N24 H242 N H sing 1.01 N N
79 C14 O33 C O sing 1.43 N N
80 C14 O54 C O sing 1.43 N N
81 C14 H14 C H sing 1.09 N N
82 C54 O54 C O sing 1.43 N N
83 C54 C64 C C sing 1.53 N N
84 C54 H54 C H sing 1.09 N N
85 C64 N64 C N sing 1.47 N N
86 C64 H11A C H sing 1.09 N N
87 C64 H12A C H sing 1.09 N N
88 N64 H641 N H sing 1.01 N N
89 N64 H642 N H sing 1.01 N N
90 C15 C25 C C sing 1.53 N N
91 C15 O55 C O sing 1.43 N N
92 C15 H15 C H sing 1.09 N N
93 C25 C35 C C sing 1.53 N N
94 C25 O25 C O sing 1.43 N N
95 C25 H25 C H sing 1.09 N N
96 C35 C45 C C sing 1.53 N N
97 C35 O35 C O sing 1.43 N N
98 C35 H35 C H sing 1.09 N N
99 C45 C55 C C sing 1.53 N N
100 C45 O45 C O sing 1.43 N N
101 C45 H45 C H sing 1.09 N N
102 C55 C65 C C sing 1.53 N N
103 C55 O55 C O sing 1.43 N N
104 C55 H55 C H sing 1.09 N N
105 C65 O65 C O sing 1.43 N N
106 C65 H651 C H sing 1.09 N N
107 C65 H652 C H sing 1.09 N N
108 O25 H7 O H sing 0.97 N N
109 O35 H6 O H sing 0.97 N N
110 O45 H5 O H sing 0.97 N N
111 O65 H65 O H sing 0.97 N N



LIV : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
LIV 2esj Open in New Window Bound ligand 2 1
LIV 2fd0 Open in New Window Bound ligand 2 1
LIV 3c5d Open in New Window Bound ligand 2 1
LIV 6cey Open in New Window Bound ligand 1 1