Chemical Components in the PDB

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SJP : Summary

Code

SJP

One-letter code

X

Molecule name

(2R,3R)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-{[3-O-(2,6-diamino-2,3,4,6-tetradeoxy-beta-L-threo-hexopyranosyl)-beta-D-ribofuranosyl]oxy}-2-hydroxycyclohexyl]-3-fluoro-2-hydroxybutanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (2R,3R)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-{[3-O-(2,6-diamino-2,3,4,6-tetradeoxy-beta-L-threo-hexopyranosyl)-beta-D-ribofuranosyl]oxy}-2-hydroxycyclohexyl]-3-fluoro-2-hydroxybutanamide
OpenEye OEToolkits 1.7.6 (2R,3R)-N-[(1R,2S,3R,4R,5S)-4-[(2R,3R,6S)-6-(aminomethyl)-3-azanyl-oxan-2-yl]oxy-3-[(2S,3R,4S,5R)-4-[(2R,3R,6R)-6-(aminomethyl)-3-azanyl-oxan-2-yl]oxy-5-(hydroxymethyl)-3-oxidanyl-oxolan-2-yl]oxy-5-azanyl-2-oxidanyl-cyclohexyl]-4-azanyl-3-fluoranyl-2-oxidanyl-butanamide

Formula

C27 H52 F N7 O11

Formal charge

0

Molecular weight

669.74 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 FC(CN)C(O)C(=O)NC4C(O)C(OC2OC(C(OC1OC(CN)CCC1N)C2O)CO)C(OC3OC(CN)CCC3N)C(N)C4
SMILES CACTVS 3.385 NC[CH](F)[CH](O)C(=O)N[CH]1C[CH](N)[CH](O[CH]2O[CH](CN)CC[CH]2N)[CH](O[CH]3O[CH](CO)[CH](O[CH]4O[CH](CN)CC[CH]4N)[CH]3O)[CH]1O
SMILES OpenEye OEToolkits 1.7.6 C1CC(C(OC1CN)OC2C(CC(C(C2OC3C(C(C(O3)CO)OC4C(CCC(O4)CN)N)O)O)NC(=O)C(C(CN)F)O)N)N
Canonical SMILES CACTVS 3.385 NC[C@@H](F)[C@H](O)C(=O)N[C@@H]1C[C@H](N)[C@@H](O[C@H]2O[C@H](CN)CC[C@H]2N)[C@H](O[C@@H]3O[C@H](CO)[C@@H](O[C@H]4O[C@@H](CN)CC[C@H]4N)[C@H]3O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.6 C1C[C@H]([C@H](O[C@@H]1CN)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](CC[C@@H](O4)CN)N)O)O)NC(=O)[C@H]([C@@H](CN)F)O)N)N

IUPAC InChI

InChI=1S/C27H52FN7O11/c28-12(8-31)18(37)24(40)35-16-5-15(34)21(44-25-13(32)3-1-10(6-29)41-25)23(19(16)38)46-27-20(39)22(17(9-36)43-27)45-26-14(33)4-2-11(7-30)42-26/h10-23,25-27,36-39H,1-9,29-34H2,(H,35,40)/t10-,11+,12+,13+,14+,15-,16+,17+,18-,19-,20+,21+,22+,23+,25+,26+,27-/m0/s1

IUPAC InChI key

XWTWBGQMVSXRIE-ZLDKHCKJSA-N
SJP

wwPDB Information

Atom count

98 (46 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-03-05

Last modified at

2020-06-01

Status

Released

Obsoleted

Not Assigned



SJP : Atoms of Molecule

Total Number of Atoms: 98
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 0.585 3.485 1.144
2 C10 C C10 R N N 0 1.694 1.497 0.394
3 C11 C C11 R N N 0 1.044 0.178 -0.028
4 C12 C C12 S N N 0 1.973 -0.985 0.327
5 C13 C C13 S N N 0 -1.175 -0.727 -0.072
6 C14 C C14 R N N 0 -2.466 -0.886 0.761
7 C15 C C15 S N N 0 -3.602 -0.776 -0.281
8 C16 C C16 R N N 0 -2.863 -0.564 -1.62
9 C17 C C17 N N N 0 -3.638 0.411 -2.508
10 C18 C C18 R N N 0 -5.493 -1.983 0.563
11 C19 C C19 R N N 0 -6.088 -3.392 0.631
12 C2 C C2 R N N 0 -0.783 4.148 0.96
13 C20 C C20 N N N 0 -7.33 -3.371 1.528
14 C21 C C21 N N N 0 -8.326 -2.345 0.978
15 C22 C C22 R N N 0 -7.644 -0.976 0.897
16 C23 C C23 N N N 0 -8.614 0.041 0.293
17 C24 C C24 R N N 0 6.919 -3.069 0.666
18 C26 C C26 N N N 0 5.176 -2.291 -0.917
19 C27 C C27 N N N 0 7.935 -4.178 0.946
20 C28 C C28 R N N 0 6.091 -3.436 -0.567
21 C3 C C3 N N N 0 -0.775 4.966 -0.335
22 C4 C C4 N N N 0 0.363 5.99 -0.272
23 C5 C C5 S N N 0 1.687 5.256 -0.041
24 C6 C C6 N N N 0 2.821 6.275 0.083
25 C7 C C7 R N N 0 3.305 -0.816 -0.407
26 C8 C C8 N N N 0 3.955 0.504 0.014
27 C9 C C9 S N N 0 3.026 1.666 -0.34
28 F99 F F99 N N N 0 7.595 -1.866 0.433
29 N19 N N19 N N N 0 -7.96 1.355 0.215
30 N2 N N2 N N N 0 -1.823 3.114 0.881
31 N23 N N23 N N N 0 -6.465 -3.83 -0.719
32 N3 N N3 N N N 0 8.73 -3.826 2.13
33 N6 N N6 N N N 0 4.08 5.575 0.371
34 N7 N N7 N N N 0 4.194 -1.929 -0.067
35 N9 N N9 N N N 0 3.65 2.933 0.064
36 O1 O O1 N N N 0 0.826 2.583 0.062
37 O11 O O11 N N N 0 -0.2 0.02 0.658
38 O12 O O12 N N N 0 1.365 -2.217 -0.066
39 O14 O O14 N N N 0 -2.494 -2.162 1.404
40 O16 O O16 N N N 0 -1.585 -0.002 -1.252
41 O17 O O17 N N N 0 -3.001 0.504 -3.784
42 O18 O O18 N N N 0 -4.367 -1.982 -0.316
43 O19 O O19 N N N 0 6.965 -3.7 -1.667
44 O2 O O2 N N N 0 5.323 -1.695 -1.963
45 O22 O O22 N N N 0 -6.48 -1.073 0.074
46 O5 O O5 N N N 0 1.601 4.49 1.163
47 H1 H H1 N N N 0 0.599 2.936 2.085
48 H2 H H2 N N N 0 1.871 1.488 1.469
49 H3 H H3 N N N 0 0.867 0.187 -1.103
50 H4 H H4 N N N 0 2.149 -0.994 1.403
51 H5 H H5 N N N 0 -0.776 -1.704 -0.347
52 H6 H H6 N N N 0 -2.545 -0.087 1.498
53 H7 H H7 N N N 0 -4.242 0.077 -0.059
54 H8 H H8 N N N 0 -2.726 -1.516 -2.133
55 H9 H H9 N N N 0 -4.659 0.052 -2.637
56 H10 H H10 N N N 0 -3.655 1.395 -2.038
57 H11 H H11 N N N 0 -5.176 -1.673 1.56
58 H12 H H12 N N N 0 -5.35 -4.079 1.045
59 H13 H H13 N N N 0 -0.985 4.806 1.806
60 H14 H H14 N N N 0 -7.791 -4.358 1.535
61 H15 H H15 N N N 0 -7.043 -3.093 2.542
62 H16 H H16 N N N 0 -8.651 -2.649 -0.017
63 H17 H H17 N N N 0 -9.189 -2.283 1.641
64 H18 H H18 N N N 0 -7.356 -0.654 1.898
65 H19 H H19 N N N 0 -8.901 -0.281 -0.708
66 H20 H H20 N N N 0 -9.502 0.115 0.921
67 H21 H H21 N N N 0 6.259 -2.954 1.526
68 H22 H H22 N N N 0 7.408 -5.115 1.128
69 H24 H H24 N N N 0 5.496 -4.324 -0.355
70 H23 H H23 N N N 0 8.595 -4.293 0.086
71 H25 H H25 N N N 0 -0.622 4.302 -1.185
72 H26 H H26 N N N 0 -1.727 5.486 -0.443
73 H27 H H27 N N N 0 0.411 6.539 -1.212
74 H28 H H28 N N N 0 0.183 6.685 0.548
75 H29 H H29 N N N 0 1.885 4.591 -0.881
76 H30 H H30 N N N 0 2.917 6.826 -0.852
77 H31 H H31 N N N 0 2.598 6.97 0.893
78 H32 H H32 N N N 0 3.128 -0.807 -1.482
79 H33 H H33 N N N 0 4.131 0.495 1.09
80 H34 H H34 N N N 0 4.904 0.624 -0.508
81 H35 H H35 N N N 0 2.85 1.675 -1.416
82 H36 H H36 N N N 0 -7.099 1.299 -0.308
83 H37 H H37 N N N 0 -8.58 2.045 -0.181
84 H39 H H39 N N N 0 -2.735 3.527 0.76
85 H40 H H40 N N N 0 -1.623 2.456 0.143
86 H42 H H42 N N N 0 -6.86 -4.759 -0.701
87 H43 H H43 N N N 0 -7.101 -3.175 -1.148
88 H45 H H45 N N N 0 8.135 -3.651 2.926
89 H46 H H46 N N N 0 9.408 -4.544 2.337
90 H48 H H48 N N N 0 4.856 6.219 0.39
91 H49 H H49 N N N 0 4.017 5.058 1.235
92 H51 H H51 N N N 0 4.077 -2.406 0.77
93 H52 H H52 N N N 0 4.578 3.019 -0.323
94 H53 H H53 N N N 0 3.075 3.72 -0.198
95 H55 H H55 N N N 0 1.9 -2.999 0.129
96 H56 H H56 N N N 0 -1.766 -2.306 2.025
97 H57 H H57 N N N 0 -3.44 1.106 -4.4
98 H58 H H58 N N N 0 7.525 -2.951 -1.912



SJP : Chemical Bonds

Total Number of Bonds: 101
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C20 C19 C C sing 1.53 N N
2 C20 C21 C C sing 1.53 N N
3 C19 N23 C N sing 1.47 N N
4 C19 C18 C C sing 1.53 N N
5 C21 C22 C C sing 1.53 N N
6 C18 O18 C O sing 1.43 N N
7 C18 O22 C O sing 1.43 N N
8 C22 O22 C O sing 1.43 N N
9 C22 C23 C C sing 1.53 N N
10 O18 C15 O C sing 1.43 N N
11 O14 C14 O C sing 1.43 N N
12 C23 N19 C N sing 1.47 N N
13 C15 C14 C C sing 1.55 N N
14 C15 C16 C C sing 1.54 N N
15 C14 C13 C C sing 1.54 N N
16 F99 C24 F C sing 1.4 N N
17 N3 C27 N C sing 1.47 N N
18 C16 C17 C C sing 1.53 N N
19 C16 O16 C O sing 1.44 N N
20 C13 O16 C O sing 1.44 N N
21 C13 O11 C O sing 1.43 N N
22 O12 C12 O C sing 1.43 N N
23 C27 C24 C C sing 1.53 N N
24 C17 O17 C O sing 1.43 N N
25 C24 C28 C C sing 1.53 N N
26 O19 C28 O C sing 1.43 N N
27 O11 C11 O C sing 1.43 N N
28 C12 C11 C C sing 1.53 N N
29 C12 C7 C C sing 1.53 N N
30 C28 C26 C C sing 1.51 N N
31 N7 C26 N C sing 1.35 N N
32 N7 C7 N C sing 1.46 N N
33 C11 C10 C C sing 1.53 N N
34 C26 O2 C O doub 1.21 N N
35 C7 C8 C C sing 1.53 N N
36 C10 O1 C O sing 1.43 N N
37 C10 C9 C C sing 1.53 N N
38 C1 O1 C O sing 1.43 N N
39 C1 O5 C O sing 1.43 N N
40 C1 C2 C C sing 1.53 N N
41 N2 C2 N C sing 1.47 N N
42 C8 C9 C C sing 1.53 N N
43 O5 C5 O C sing 1.43 N N
44 C2 C3 C C sing 1.53 N N
45 C9 N9 C N sing 1.47 N N
46 N6 C6 N C sing 1.47 N N
47 C5 C6 C C sing 1.53 N N
48 C5 C4 C C sing 1.53 N N
49 C3 C4 C C sing 1.53 N N
50 C1 H1 C H sing 1.09 N N
51 C10 H2 C H sing 1.09 N N
52 C11 H3 C H sing 1.09 N N
53 C12 H4 C H sing 1.09 N N
54 C13 H5 C H sing 1.09 N N
55 C14 H6 C H sing 1.09 N N
56 C15 H7 C H sing 1.09 N N
57 C16 H8 C H sing 1.09 N N
58 C17 H9 C H sing 1.09 N N
59 C17 H10 C H sing 1.09 N N
60 C18 H11 C H sing 1.09 N N
61 C19 H12 C H sing 1.09 N N
62 C2 H13 C H sing 1.09 N N
63 C20 H14 C H sing 1.09 N N
64 C20 H15 C H sing 1.09 N N
65 C21 H16 C H sing 1.09 N N
66 C21 H17 C H sing 1.09 N N
67 C22 H18 C H sing 1.09 N N
68 C23 H19 C H sing 1.09 N N
69 C23 H20 C H sing 1.09 N N
70 C24 H21 C H sing 1.09 N N
71 C27 H22 C H sing 1.09 N N
72 C27 H23 C H sing 1.09 N N
73 C28 H24 C H sing 1.09 N N
74 C3 H25 C H sing 1.09 N N
75 C3 H26 C H sing 1.09 N N
76 C4 H27 C H sing 1.09 N N
77 C4 H28 C H sing 1.09 N N
78 C5 H29 C H sing 1.09 N N
79 C6 H30 C H sing 1.09 N N
80 C6 H31 C H sing 1.09 N N
81 C7 H32 C H sing 1.09 N N
82 C8 H33 C H sing 1.09 N N
83 C8 H34 C H sing 1.09 N N
84 C9 H35 C H sing 1.09 N N
85 N19 H36 N H sing 1.01 N N
86 N19 H37 N H sing 1.01 N N
87 N2 H39 N H sing 1.01 N N
88 N2 H40 N H sing 1.01 N N
89 N23 H42 N H sing 1.01 N N
90 N23 H43 N H sing 1.01 N N
91 N3 H45 N H sing 1.01 N N
92 N3 H46 N H sing 1.01 N N
93 N6 H48 N H sing 1.01 N N
94 N6 H49 N H sing 1.01 N N
95 N7 H51 N H sing 0.97 N N
96 N9 H52 N H sing 1.01 N N
97 N9 H53 N H sing 1.01 N N
98 O12 H55 O H sing 0.97 N N
99 O14 H56 O H sing 0.97 N N
100 O17 H57 O H sing 0.97 N N
101 O19 H58 O H sing 0.97 N N



SJP : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
SJP 3wru Open in New Window Bound ligand 2 1