Chemical Components in the PDB

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NMZ : Summary

Code

NMZ

One-letter code

X

Molecule name

(2S)-4-amino-N-{(1R,2S,3R,4R,5S)-5-amino-3-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy }-4-[(2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranosyl)oxy]-2-hydroxycyclohexyl}-2-hydroxybutanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-4-amino-N-{(1R,2S,3R,4R,5S)-5-amino-3-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-4-[(2,6-diamino-2,4,6-trideoxy-4-fluoro-alpha-D-galactopyranosyl)oxy]-2-hydroxycyclohexyl}-2-hydroxybutanamide
OpenEye OEToolkits 1.9.2 (2S)-N-[(1R,2S,3R,4R,5S)-3-[(2S,3R,4S,5R)-4-[(2R,3R,4R,5S,6S)-6-(aminomethyl)-3-azanyl-4,5-bis(oxidanyl)oxan-2-yl]oxy-5-(hydroxymethyl)-3-oxidanyl-oxolan-2-yl]oxy-4-[(2S,3R,4R,5R,6R)-6-(aminomethyl)-3-azanyl-5-fluoranyl-4-oxidanyl-oxan-2-yl]oxy-5-azanyl-2-oxidanyl-cyclohexyl]-4-azanyl-2-oxidanyl-butanamide

Formula

C27 H52 F N7 O14

Formal charge

0

Molecular weight

717.739 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 FC1C(O)C(N)C(OC1CN)OC4C(N)CC(NC(=O)C(O)CCN)C(O)C4OC3OC(C(OC2OC(CN)C(O)C(O)C2N)C3O)CO
SMILES CACTVS 3.385 NCC[CH](O)C(=O)N[CH]1C[CH](N)[CH](O[CH]2O[CH](CN)[CH](F)[CH](O)[CH]2N)[CH](O[CH]3O[CH](CO)[CH](O[CH]4O[CH](CN)[CH](O)[CH](O)[CH]4N)[CH]3O)[CH]1O
SMILES OpenEye OEToolkits 1.9.2 C1C(C(C(C(C1NC(=O)C(CCN)O)O)OC2C(C(C(O2)CO)OC3C(C(C(C(O3)CN)O)O)N)O)OC4C(C(C(C(O4)CN)F)O)N)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](F)[C@H](O)[C@H]2N)[C@H](O[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)[C@H]1O
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)O[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O[C@@H]3[C@@H]([C@H]([C@@H]([C@@H](O3)CN)O)O)N)O)O[C@@H]4[C@@H]([C@H]([C@H]([C@H](O4)CN)F)O)N)N

IUPAC InChI

InChI=1S/C27H52FN7O14/c28-13-10(4-30)44-25(14(33)18(13)40)47-21-7(32)3-8(35-24(43)9(37)1-2-29)16(38)23(21)49-27-20(42)22(12(6-36)46-27)48-26-15(34)19(41)17(39)11(5-31)45-26/h7-23,25-27,36-42H,1-6,29-34H2,(H,35,43)/t7-,8+,9-,10+,11-,12+,13-,14+,15+,16-,17+,18-,19+,20+,21+,22+,23+,25+,26+,27-/m0/s1

IUPAC InChI key

VWXJAOATJPQONW-MKAHEPKYSA-N
NMZ

wwPDB Information

Atom count

101 (49 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-05-16

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



NMZ : Atoms of Molecule

Total Number of Atoms: 101
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 R N N 0 -1.462 -5.672 -0.199
2 C5 C C2 R N N 0 -2.708 -4.83 0.089
3 C6 C C3 N N N 0 -3.903 -5.754 0.334
4 C3 C C4 R N N 0 -0.259 -4.742 -0.383
5 C2 C C5 R N N 0 -0.099 -3.878 0.872
6 C1 C C6 S N N 0 -1.398 -3.106 1.119
7 O1 O O1 N N N 0 -1.648 -2.23 0.018
8 O2 O O2 N N N 0 -5.752 2.453 -1.943
9 C10 C C7 R N N 0 -2.403 -1.066 0.361
10 C11 C C8 R N N 0 -1.638 0.185 -0.074
11 C12 C C9 S N N 0 -2.447 1.431 0.294
12 C13 C C10 S N N 0 0.656 0.876 -0.157
13 C14 C C11 R N N 0 1.969 0.913 0.656
14 C15 C C12 S N N 0 3.072 0.695 -0.404
15 C16 C C13 R N N 0 2.295 0.553 -1.732
16 C17 C C14 N N N 0 2.961 -0.49 -2.631
17 C18 C C15 R N N 0 5.083 1.718 0.406
18 C19 C C16 R N N 0 5.809 3.065 0.461
19 C20 C C17 R N N 0 7.058 2.927 1.337
20 C21 C C18 S N N 0 7.943 1.811 0.774
21 C22 C C19 S N N 0 7.134 0.513 0.707
22 C23 C C20 N N N 0 7.993 -0.592 0.09
23 C24 C C21 N N N 0 -7.168 3.974 0.708
24 C26 C C22 N N N 0 -5.532 3.033 -0.901
25 C27 C C23 N N N 0 -7.88 5.255 1.148
26 C28 C C24 S N N 0 -6.329 4.26 -0.539
27 C7 C C25 R N N 0 -3.801 1.388 -0.418
28 C8 C C26 N N N 0 -4.566 0.137 0.016
29 C9 C C27 S N N 0 -3.757 -1.109 -0.351
30 F99 F F1 N N N 0 -1.225 -6.538 0.874
31 N19 N N1 N N N 0 7.217 -1.838 0.026
32 N2 N N2 N N N 0 1.006 -2.93 0.678
33 N23 N N3 N N N 0 6.204 3.465 -0.896
34 N3 N N4 N N N 0 -8.686 4.98 2.345
35 N6 N N5 N N N 0 -5.126 -4.95 0.461
36 N7 N N6 N N N 0 -4.575 2.581 -0.067
37 N9 N N7 N N N 0 -4.492 -2.311 0.066
38 O11 O O3 N N N 0 -0.374 0.226 0.591
39 O12 O O4 N N N 0 -1.732 2.6 -0.112
40 O14 O O5 N N N 0 2.129 2.182 1.292
41 O16 O O6 N N N 0 0.975 0.114 -1.341
42 O17 O O7 N N N 0 2.298 -0.522 -3.896
43 O18 O O8 N N N 0 3.947 1.824 -0.455
44 O19 O O9 N N N 0 -7.192 4.605 -1.625
45 O22 O O10 N N N 0 5.971 0.719 -0.097
46 O23 O O11 N N N 0 0.922 -5.522 -0.579
47 O24 O O12 N N N 0 8.385 2.168 -0.537
48 O25 O O13 N N N 0 6.67 2.601 2.674
49 O5 O O14 N N N 0 -2.481 -4.028 1.25
50 H1 H H1 N N N 0 -1.616 -6.253 -1.108
51 H2 H H2 N N N 0 -2.916 -4.185 -0.764
52 H3 H H3 N N N 0 -4.007 -6.443 -0.505
53 H4 H H4 N N N 0 -3.743 -6.321 1.251
54 H5 H H5 N N N 0 -0.422 -4.102 -1.25
55 H6 H H6 N N N 0 0.115 -4.516 1.729
56 H7 H H7 N N N 0 -1.305 -2.522 2.034
57 H8 H H8 N N N 0 -2.56 -1.04 1.439
58 H9 H H9 N N N 0 -1.481 0.159 -1.152
59 H10 H H10 N N N 0 -2.604 1.457 1.372
60 H11 H H11 N N N 0 0.348 1.887 -0.427
61 H12 H H12 N N N 0 1.984 0.112 1.395
62 H13 H H13 N N N 0 3.634 -0.213 -0.19
63 H14 H H14 N N N 0 2.239 1.514 -2.243
64 H15 H H15 N N N 0 4.009 -0.227 -2.776
65 H16 H H16 N N N 0 2.895 -1.471 -2.16
66 H17 H H17 N N N 0 4.755 1.441 1.408
67 H18 H H18 N N N 0 5.147 3.819 0.886
68 H19 H H19 N N N 0 7.61 3.866 1.335
69 H20 H H20 N N N 0 8.807 1.669 1.423
70 H21 H H21 N N N 0 6.833 0.22 1.713
71 H22 H H22 N N N 0 8.294 -0.3 -0.916
72 H23 H H23 N N N 0 8.88 -0.749 0.703
73 H24 H H24 N N N 0 -6.518 3.626 1.51
74 H25 H H25 N N N 0 -7.907 3.207 0.48
75 H26 H H26 N N N 0 -7.14 6.022 1.376
76 H27 H H27 N N N 0 -8.53 5.603 0.345
77 H28 H H28 N N N 0 -5.649 5.089 -0.338
78 H29 H H29 N N N 0 -3.644 1.362 -1.497
79 H30 H H30 N N N 0 -4.723 0.163 1.095
80 H31 H H31 N N N 0 -5.53 0.106 -0.491
81 H32 H H32 N N N 0 -3.6 -1.135 -1.429
82 H33 H H33 N N N 0 6.356 -1.702 -0.484
83 H34 H H34 N N N 0 7.762 -2.584 -0.379
84 H36 H H36 N N N 0 1.874 -3.417 0.508
85 H37 H H37 N N N 0 0.802 -2.284 -0.07
86 H39 H H39 N N N 0 5.397 3.557 -1.495
87 H40 H H40 N N N 0 6.741 4.319 -0.879
88 H42 H H42 N N N 0 -9.166 5.811 2.656
89 H43 H H43 N N N 0 -9.336 4.227 2.179
90 H45 H H45 N N N 0 -5.352 -4.496 -0.41
91 H46 H H46 N N N 0 -5.897 -5.514 0.786
92 H48 H H48 N N N 0 -4.4 3.045 0.767
93 H49 H H49 N N N 0 -5.376 -2.379 -0.414
94 H50 H H50 N N N 0 -3.938 -3.141 -0.077
95 H52 H H52 N N N 0 -2.187 3.429 0.089
96 H53 H H53 N N N 0 1.43 2.396 1.924
97 H54 H H54 N N N 0 2.668 -1.163 -4.518
98 H55 H H55 N N N 0 -7.825 3.912 -1.86
99 H56 H H56 N N N 0 0.888 -6.1 -1.354
100 H57 H H57 N N N 0 8.901 2.985 -0.57
101 H58 H H58 N N N 0 7.413 2.498 3.285



NMZ : Chemical Bonds

Total Number of Bonds: 104
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N6 C6 N C sing 1.47 N N
2 C6 C5 C C sing 1.53 N N
3 N9 C9 N C sing 1.47 N N
4 C5 C4 C C sing 1.53 N N
5 C5 O5 C O sing 1.43 N N
6 C4 F99 C F sing 1.4 N N
7 C4 C3 C C sing 1.53 N N
8 C9 C8 C C sing 1.53 N N
9 C9 C10 C C sing 1.53 N N
10 C8 C7 C C sing 1.53 N N
11 C3 O23 C O sing 1.43 N N
12 C3 C2 C C sing 1.53 N N
13 O5 C1 O C sing 1.43 N N
14 O1 C10 O C sing 1.43 N N
15 O1 C1 O C sing 1.43 N N
16 O19 C28 O C sing 1.43 N N
17 C10 C11 C C sing 1.53 N N
18 O2 C26 O C doub 1.21 N N
19 C28 C26 C C sing 1.51 N N
20 C28 C24 C C sing 1.53 N N
21 C26 N7 C N sing 1.35 N N
22 C1 C2 C C sing 1.53 N N
23 N7 C7 N C sing 1.46 N N
24 C7 C12 C C sing 1.53 N N
25 C2 N2 C N sing 1.47 N N
26 C27 C24 C C sing 1.53 N N
27 C27 N3 C N sing 1.47 N N
28 C11 C12 C C sing 1.53 N N
29 C11 O11 C O sing 1.43 N N
30 C12 O12 C O sing 1.43 N N
31 O11 C13 O C sing 1.43 N N
32 C13 O16 C O sing 1.44 N N
33 C13 C14 C C sing 1.54 N N
34 O16 C16 O C sing 1.44 N N
35 O17 C17 O C sing 1.43 N N
36 C17 C16 C C sing 1.53 N N
37 C14 O14 C O sing 1.43 N N
38 C14 C15 C C sing 1.55 N N
39 C16 C15 C C sing 1.55 N N
40 C15 O18 C O sing 1.43 N N
41 O18 C18 O C sing 1.43 N N
42 C18 O22 C O sing 1.43 N N
43 C18 C19 C C sing 1.53 N N
44 O22 C22 O C sing 1.43 N N
45 N19 C23 N C sing 1.47 N N
46 N23 C19 N C sing 1.47 N N
47 C19 C20 C C sing 1.53 N N
48 C23 C22 C C sing 1.53 N N
49 C22 C21 C C sing 1.53 N N
50 O24 C21 O C sing 1.43 N N
51 C20 C21 C C sing 1.53 N N
52 C20 O25 C O sing 1.43 N N
53 C4 H1 C H sing 1.09 N N
54 C5 H2 C H sing 1.09 N N
55 C6 H3 C H sing 1.09 N N
56 C6 H4 C H sing 1.09 N N
57 C3 H5 C H sing 1.09 N N
58 C2 H6 C H sing 1.09 N N
59 C1 H7 C H sing 1.09 N N
60 C10 H8 C H sing 1.09 N N
61 C11 H9 C H sing 1.09 N N
62 C12 H10 C H sing 1.09 N N
63 C13 H11 C H sing 1.09 N N
64 C14 H12 C H sing 1.09 N N
65 C15 H13 C H sing 1.09 N N
66 C16 H14 C H sing 1.09 N N
67 C17 H15 C H sing 1.09 N N
68 C17 H16 C H sing 1.09 N N
69 C18 H17 C H sing 1.09 N N
70 C19 H18 C H sing 1.09 N N
71 C20 H19 C H sing 1.09 N N
72 C21 H20 C H sing 1.09 N N
73 C22 H21 C H sing 1.09 N N
74 C23 H22 C H sing 1.09 N N
75 C23 H23 C H sing 1.09 N N
76 C24 H24 C H sing 1.09 N N
77 C24 H25 C H sing 1.09 N N
78 C27 H26 C H sing 1.09 N N
79 C27 H27 C H sing 1.09 N N
80 C28 H28 C H sing 1.09 N N
81 C7 H29 C H sing 1.09 N N
82 C8 H30 C H sing 1.09 N N
83 C8 H31 C H sing 1.09 N N
84 C9 H32 C H sing 1.09 N N
85 N19 H33 N H sing 1.01 N N
86 N19 H34 N H sing 1.01 N N
87 N2 H36 N H sing 1.01 N N
88 N2 H37 N H sing 1.01 N N
89 N23 H39 N H sing 1.01 N N
90 N23 H40 N H sing 1.01 N N
91 N3 H42 N H sing 1.01 N N
92 N3 H43 N H sing 1.01 N N
93 N6 H45 N H sing 1.01 N N
94 N6 H46 N H sing 1.01 N N
95 N7 H48 N H sing 0.97 N N
96 N9 H49 N H sing 1.01 N N
97 N9 H50 N H sing 1.01 N N
98 O12 H52 O H sing 0.97 N N
99 O14 H53 O H sing 0.97 N N
100 O17 H54 O H sing 0.97 N N
101 O19 H55 O H sing 0.97 N N
102 O23 H56 O H sing 0.97 N N
103 O24 H57 O H sing 0.97 N N
104 O25 H58 O H sing 0.97 N N



NMZ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
NMZ 4pdq Open in New Window Bound ligand 1 1