Chemical Components in the PDB

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LUJ : Summary

Code

LUJ

One-letter code

X

Molecule name

(1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxyc yclohexyl 2-amino-2,4-dideoxy-4-propyl-alpha-D-glucopyranoside

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2,4-dideoxy-4-propyl-alpha-D-glucopyranoside
OpenEye OEToolkits 2.0.7 (2~{S},3~{S},4~{R},5~{R},6~{R})-2-(aminomethyl)-5-azanyl-6-[(2~{R},3~{S},4~{R},5~{S})-5-[(1~{R},2~{R},3~{S},5~{R},6~{S})-3,5-bis(azanyl)-2-[(2~{R},3~{R},4~{S},5~{S},6~{S})-3-azanyl-6-(hydroxymethyl)-4-oxidanyl-5-propyl-oxan-2-yl]oxy-6-oxidanyl-cyclohexyl]oxy-2-(hydroxymethyl)-4-oxidanyl-oxolan-3-yl]oxy-oxane-3,4-diol

Formula

C26 H51 N5 O13

Formal charge

0

Molecular weight

641.709 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 CCCC1C(CO)OC(C(C1O)N)OC2C(N)CC(C(C2OC3OC(CO)C(C3O)OC4OC(CN)C(O)C(O)C4N)O)N
SMILES CACTVS 3.385 CCC[CH]1[CH](O)[CH](N)[CH](O[CH]1CO)O[CH]2[CH](N)C[CH](N)[CH](O)[CH]2O[CH]3O[CH](CO)[CH](O[CH]4O[CH](CN)[CH](O)[CH](O)[CH]4N)[CH]3O
SMILES OpenEye OEToolkits 2.0.7 CCCC1C(OC(C(C1O)N)OC2C(CC(C(C2OC3C(C(C(O3)CO)OC4C(C(C(C(O4)CN)O)O)N)O)O)N)N)CO
Canonical SMILES CACTVS 3.385 CCC[C@H]1[C@H](O)[C@@H](N)[C@H](O[C@@H]1CO)O[C@@H]2[C@@H](N)C[C@@H](N)[C@H](O)[C@H]2O[C@@H]3O[C@H](CO)[C@@H](O[C@H]4O[C@@H](CN)[C@@H](O)[C@H](O)[C@H]4N)[C@H]3O
Canonical SMILES OpenEye OEToolkits 2.0.7 CCC[C@@H]1[C@H](O[C@@H]([C@@H]([C@H]1O)N)O[C@@H]2[C@H](C[C@H]([C@@H]([C@H]2O[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)O)N)O)O)N)N)CO

IUPAC InChI

InChI=1S/C26H51N5O13/c1-2-3-8-12(6-32)40-24(14(30)16(8)34)42-21-10(29)4-9(28)17(35)23(21)44-26-20(38)22(13(7-33)41-26)43-25-15(31)19(37)18(36)11(5-27)39-25/h8-26,32-38H,2-7,27-31H2,1H3/t8-,9-,10+,11+,12-,13-,14-,15-,16+,17+,18-,19-,20-,21-,22-,23-,24-,25-,26+/m1/s1

IUPAC InChI key

GSHRTHLCTXGYPA-RNNXBIGMSA-N
LUJ

wwPDB Information

Atom count

95 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-03-14

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



LUJ : Atoms of Molecule

Total Number of Atoms: 95
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CBR C C1 N N N 0 5.446 -5.646 1.834
2 CBQ C C2 N N N 0 4.734 -4.866 0.727
3 CBP C C3 N N N 0 5.224 -3.417 0.729
4 CBG C C4 S N N 0 4.621 -2.673 -0.464
5 CBI C C5 S N N 0 5.235 -1.273 -0.558
6 OAF O O1 N N N 0 4.629 -0.56 -1.638
7 CBN C C6 N N N 0 6.74 -1.391 -0.805
8 OAM O O2 N N N 0 7.324 -0.087 -0.82
9 CBE C C7 S N N 0 3.106 -2.548 -0.278
10 OAI O O3 N N N 0 2.517 -3.85 -0.264
11 CBD C C8 R N N 0 2.525 -1.735 -1.439
12 NAP N N1 N N N 0 1.083 -1.546 -1.233
13 CBC C C9 R N N 0 3.22 -0.37 -1.494
14 OAB O O4 N N N 0 2.957 0.348 -0.287
15 CAT C C10 R N N 0 2.989 1.769 -0.438
16 CAU C C11 S N N 0 4.208 2.332 0.295
17 NAN N N2 N N N 0 5.432 1.752 -0.273
18 CAX C C12 N N N 0 4.242 3.853 0.134
19 CAW C C13 R N N 0 2.967 4.458 0.725
20 NAO N N3 N N N 0 3.0 5.918 0.57
21 CAV C C14 S N N 0 1.748 3.895 -0.008
22 OAE O O5 N N N 0 0.557 4.459 0.544
23 CAS C C15 R N N 0 1.714 2.374 0.153
24 O1' O O6 N N N 0 0.575 1.847 -0.531
25 C1' C C16 S N N 0 -0.601 1.765 0.275
26 C2' C C17 R N N 0 -1.788 1.23 -0.557
27 O2' O O7 N N N 0 -2.61 2.309 -1.006
28 O4' O O8 N N N 0 -0.422 0.792 1.328
29 C4' C C18 R N N 0 -1.757 0.43 1.744
30 C5' C C19 N N N 0 -1.743 -0.92 2.463
31 O5' O O9 N N N 0 -1.027 -0.797 3.693
32 C3' C C20 S N N 0 -2.565 0.332 0.431
33 O3' O O10 N N N 0 -3.892 0.829 0.622
34 CBF C C21 R N N 0 -4.855 0.273 -0.275
35 OAG O O11 N N N 0 -5.077 -1.099 0.055
36 CBM C C22 S N N 0 -6.01 -1.762 -0.801
37 CBO C C23 N N N 0 -6.146 -3.225 -0.373
38 NAR N N4 N N N 0 -4.838 -3.886 -0.468
39 CBL C C24 S N N 0 -7.373 -1.072 -0.7
40 OAL O O12 N N N 0 -7.864 -1.178 0.638
41 CBJ C C25 R N N 0 -7.217 0.406 -1.072
42 OAJ O O13 N N N 0 -6.79 0.514 -2.431
43 CBH C C26 R N N 0 -6.172 1.045 -0.153
44 NAQ N N5 N N N 0 -6.644 0.994 1.238
45 H1 H H1 N N N 0 5.226 -5.19 2.799
46 H2 H H2 N N N 0 5.097 -6.679 1.833
47 H3 H H3 N N N 0 6.521 -5.626 1.66
48 H4 H H4 N N N 0 4.954 -5.322 -0.238
49 H5 H H5 N N N 0 3.658 -4.887 0.902
50 H6 H H6 N N N 0 4.914 -2.93 1.654
51 H7 H H7 N N N 0 6.311 -3.4 0.657
52 H8 H H8 N N N 0 4.831 -3.225 -1.381
53 H9 H H9 N N N 0 5.061 -0.737 0.375
54 H10 H H10 N N N 0 7.194 -1.983 -0.01
55 H11 H H11 N N N 0 6.914 -1.879 -1.764
56 H12 H H12 N N N 0 8.279 -0.086 -0.972
57 H13 H H13 N N N 0 2.895 -2.042 0.664
58 H14 H H14 N N N 0 1.557 -3.846 -0.149
59 H15 H H15 N N N 0 2.693 -2.267 -2.376
60 H16 H H16 N N N 0 0.677 -1.012 -1.987
61 H17 H H17 N N N 0 0.614 -2.433 -1.125
62 H19 H H19 N N N 0 2.841 0.196 -2.345
63 H20 H H20 N N N 0 3.053 2.021 -1.497
64 H21 H H21 N N N 0 4.144 2.08 1.354
65 H22 H H22 N N N 0 6.254 2.156 0.15
66 H23 H H23 N N N 0 5.434 0.747 -0.178
67 H28 H H28 N N N 0 3.797 6.314 1.046
68 H25 H H25 N N N 0 5.111 4.254 0.656
69 H26 H H26 N N N 0 4.307 4.105 -0.925
70 H27 H H27 N N N 0 2.903 4.206 1.784
71 H29 H H29 N N N 0 2.995 6.179 -0.405
72 H31 H H31 N N N 0 1.812 4.146 -1.067
73 H32 H H32 N N N 0 0.511 5.423 0.477
74 H33 H H33 N N N 0 1.65 2.122 1.212
75 H34 H H34 N N N 0 -0.841 2.741 0.697
76 H35 H H35 N N N 0 -1.428 0.645 -1.403
77 H36 H H36 N N N 0 -2.154 2.938 -1.582
78 H37 H H37 N N N 0 -2.174 1.2 2.392
79 H38 H H38 N N N 0 -2.766 -1.233 2.668
80 H39 H H39 N N N 0 -1.255 -1.663 1.831
81 H40 H H40 N N N 0 -0.978 -1.617 4.203
82 H41 H H41 N N N 0 -2.59 -0.697 0.073
83 H42 H H42 N N N 0 -4.485 0.346 -1.297
84 H43 H H43 N N N 0 -5.655 -1.716 -1.83
85 H44 H H44 N N N 0 -6.502 -3.27 0.657
86 H45 H H45 N N N 0 -6.857 -3.73 -1.026
87 H46 H H46 N N N 0 -4.901 -4.854 -0.191
88 H47 H H47 N N N 0 -4.457 -3.801 -1.399
89 H49 H H49 N N N 0 -8.074 -1.549 -1.384
90 H50 H H50 N N N 0 -8.726 -0.761 0.775
91 H51 H H51 N N N 0 -8.172 0.916 -0.948
92 H52 H H52 N N N 0 -7.403 0.123 -3.069
93 H53 H H53 N N N 0 -6.014 2.083 -0.446
94 H54 H H54 N N N 0 -5.971 1.41 1.864
95 H55 H H55 N N N 0 -7.545 1.437 1.33



LUJ : Chemical Bonds

Total Number of Bonds: 98
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 NAO CAW N C sing 1.47 N N
2 OAE CAV O C sing 1.43 N N
3 CAW CAV C C sing 1.53 N N
4 CAW CAX C C sing 1.53 N N
5 NAQ CBH N C sing 1.47 N N
6 CBH CBJ C C sing 1.53 N N
7 CBH CBF C C sing 1.53 N N
8 CAV CAS C C sing 1.53 N N
9 OAJ CBJ O C sing 1.43 N N
10 CBJ CBL C C sing 1.53 N N
11 O2' C2' O C sing 1.43 N N
12 CAX CAU C C sing 1.53 N N
13 O3' CBF O C sing 1.43 N N
14 O3' C3' O C sing 1.43 N N
15 CBF OAG C O sing 1.43 N N
16 CBL OAL C O sing 1.43 N N
17 CBL CBM C C sing 1.53 N N
18 CAS O1' C O sing 1.43 N N
19 CAS CAT C C sing 1.53 N N
20 C2' C1' C C sing 1.55 N N
21 C2' C3' C C sing 1.54 N N
22 O1' C1' O C sing 1.43 N N
23 C1' O4' C O sing 1.44 N N
24 CAU CAT C C sing 1.53 N N
25 CAU NAN C N sing 1.47 N N
26 C3' C4' C C sing 1.54 N N
27 CAT OAB C O sing 1.43 N N
28 OAG CBM O C sing 1.43 N N
29 CBM CBO C C sing 1.53 N N
30 O4' C4' O C sing 1.44 N N
31 C4' C5' C C sing 1.53 N N
32 OAB CBC O C sing 1.43 N N
33 CBO NAR C N sing 1.47 N N
34 C5' O5' C O sing 1.43 N N
35 CBC OAF C O sing 1.43 N N
36 CBC CBD C C sing 1.53 N N
37 OAF CBI O C sing 1.43 N N
38 OAM CBN O C sing 1.43 N N
39 CBI CBN C C sing 1.53 N N
40 CBI CBG C C sing 1.53 N N
41 NAP CBD N C sing 1.47 N N
42 CBD CBE C C sing 1.53 N N
43 CBE CBG C C sing 1.53 N N
44 CBE OAI C O sing 1.43 N N
45 CBG CBP C C sing 1.53 N N
46 CBP CBQ C C sing 1.53 N N
47 CBQ CBR C C sing 1.53 N N
48 CBR H1 C H sing 1.09 N N
49 CBR H2 C H sing 1.09 N N
50 CBR H3 C H sing 1.09 N N
51 CBQ H4 C H sing 1.09 N N
52 CBQ H5 C H sing 1.09 N N
53 CBP H6 C H sing 1.09 N N
54 CBP H7 C H sing 1.09 N N
55 CBG H8 C H sing 1.09 N N
56 CBI H9 C H sing 1.09 N N
57 CBN H10 C H sing 1.09 N N
58 CBN H11 C H sing 1.09 N N
59 OAM H12 O H sing 0.97 N N
60 CBE H13 C H sing 1.09 N N
61 OAI H14 O H sing 0.97 N N
62 CBD H15 C H sing 1.09 N N
63 NAP H16 N H sing 1.01 N N
64 NAP H17 N H sing 1.01 N N
65 CBC H19 C H sing 1.09 N N
66 CAT H20 C H sing 1.09 N N
67 CAU H21 C H sing 1.09 N N
68 NAN H22 N H sing 1.01 N N
69 NAN H23 N H sing 1.01 N N
70 CAX H25 C H sing 1.09 N N
71 CAX H26 C H sing 1.09 N N
72 CAW H27 C H sing 1.09 N N
73 NAO H28 N H sing 1.01 N N
74 NAO H29 N H sing 1.01 N N
75 CAV H31 C H sing 1.09 N N
76 OAE H32 O H sing 0.97 N N
77 CAS H33 C H sing 1.09 N N
78 C1' H34 C H sing 1.09 N N
79 C2' H35 C H sing 1.09 N N
80 O2' H36 O H sing 0.97 N N
81 C4' H37 C H sing 1.09 N N
82 C5' H38 C H sing 1.09 N N
83 C5' H39 C H sing 1.09 N N
84 O5' H40 O H sing 0.97 N N
85 C3' H41 C H sing 1.09 N N
86 CBF H42 C H sing 1.09 N N
87 CBM H43 C H sing 1.09 N N
88 CBO H44 C H sing 1.09 N N
89 CBO H45 C H sing 1.09 N N
90 NAR H46 N H sing 1.01 N N
91 NAR H47 N H sing 1.01 N N
92 CBL H49 C H sing 1.09 N N
93 OAL H50 O H sing 0.97 N N
94 CBJ H51 C H sing 1.09 N N
95 OAJ H52 O H sing 0.97 N N
96 CBH H53 C H sing 1.09 N N
97 NAQ H54 N H sing 1.01 N N
98 NAQ H55 N H sing 1.01 N N



LUJ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
LUJ 6o97 Open in New Window Bound ligand 6 1