![spacer](http://www.ebi.ac.uk/inc/images/spacer.gif) |
NJ5 : Summary
Code ![](/pdbe/static/images/help.png)
|
NJ5
|
One-letter code ![](/pdbe/static/images/help.png)
|
X
|
Molecule name ![](/pdbe/static/images/help.png)
|
[[(2~{R},3~{S},4~{R},5~{R})-5-[2,4-bis(oxidanylidene)pyrimidin-1-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{R},4~{R},5~{S},6~{R})-3-[6-(butanoylamino)hexanoylamino]-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl] hydrogen phosphate
|
Systematic names ![](/pdbe/static/images/help.png)
|
|
Formula ![](/pdbe/static/images/help.png)
|
C25 H42 N4 O18 P2
|
Formal charge ![](/pdbe/static/images/help.png)
|
0
|
Molecular weight ![](/pdbe/static/images/help.png)
|
748.565 Da
|
SMILES ![](/pdbe/static/images/help.png)
|
Type | Program | Version | Descriptor |
SMILES
|
CACTVS |
3.385 |
CCCC(=O)NCCCCCC(=O)N[CH]1[CH](O)[CH](O)[CH](CO)O[CH]1O[P](O)(=O)O[P](O)(=O)OC[CH]2O[CH]([CH](O)[CH]2O)N3C=CC(=O)NC3=O |
SMILES
|
OpenEye OEToolkits |
2.0.7 |
CCCC(=O)NCCCCCC(=O)NC1C(C(C(OC1OP(=O)(O)OP(=O)(O)OCC2C(C(C(O2)N3C=CC(=O)NC3=O)O)O)CO)O)O |
Canonical SMILES
|
CACTVS |
3.385 |
CCCC(=O)NCCCCCC(=O)N[C@@H]1[C@@H](O)[C@H](O)[C@@H](CO)O[C@@H]1O[P](O)(=O)O[P](O)(=O)OC[C@H]2O[C@H]([C@H](O)[C@@H]2O)N3C=CC(=O)NC3=O |
Canonical SMILES
|
OpenEye OEToolkits |
2.0.7 |
CCCC(=O)NCCCCCC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@@H]1OP(=O)(O)OP(=O)(O)OC[C@@H]2[C@H]([C@H]([C@@H](O2)N3C=CC(=O)NC3=O)O)O)CO)O)O |
|
IUPAC InChI ![](/pdbe/static/images/help.png) | InChI=1S/C25H42N4O18P2/c1-2-6-15(31)26-9-5-3-4-7-16(32)27-18-21(36)19(34)13(11-30)45-24(18)46-49(41,42)47-48(39,40)43-12-14-20(35)22(37)23(44-14)29-10-8-17(33)28-25(29)38/h8,10,13-14,18-24,30,34-37H,2-7,9,11-12H2,1H3,(H,26,31)(H,27,32)(H,39,40)(H,41,42)(H,28,33,38)/t13-,14-,18-,19-,20-,21-,22-,23-,24-/m1/s1 |
IUPAC InChI key ![](/pdbe/static/images/help.png) | MGZXRAPGBJHSCZ-HDEQREAESA-N |
|
wwPDB Information |
Atom count ![](/pdbe/static/images/help.png)
|
91 (49 without Hydrogen)
|
Polymer type ![](/pdbe/static/images/help.png)
|
Bound ligand
|
Type description ![](/pdbe/static/images/help.png)
|
non-polymer
|
Type code ![](/pdbe/static/images/help.png)
|
HETAIN
|
Is modified ![](/pdbe/static/images/help.png)
|
No
|
Standard parent ![](/pdbe/static/images/help.png)
|
Not Assigned
|
Defined at ![](/pdbe/static/images/help.png)
|
2019-11-29
|
Last modified at ![](/pdbe/static/images/help.png)
|
2020-02-28
|
Status ![](/pdbe/static/images/help.png)
|
Released
|
Obsoleted ![](/pdbe/static/images/help.png)
|
Not Assigned
|
|
|
NJ5 : Atoms of Molecule
Total Number of Atoms: 91
Record |
Atom Name |
Symbol |
PDB Name |
Stereochemistry |
Is Aromatic |
Is Leaving Atom |
Charge |
X-Coordinate |
Y-Coordinate |
Z-Coordinate |
1 |
C11 |
C |
C1 |
N |
N |
N |
0 |
14.329 |
-4.771 |
-1.06 |
2 |
C12 |
C |
C2 |
N |
N |
N |
0 |
13.035 |
-4.579 |
-0.267 |
3 |
C13 |
C |
C3 |
N |
N |
N |
0 |
12.309 |
-3.329 |
-0.769 |
4 |
C14 |
C |
C4 |
N |
N |
N |
0 |
11.035 |
-3.141 |
0.013 |
5 |
C18 |
C |
C8 |
N |
N |
N |
0 |
6.242 |
0.779 |
0.291 |
6 |
O1 |
O |
O1 |
N |
N |
N |
0 |
10.736 |
-3.928 |
0.885 |
7 |
N2 |
N |
N1 |
N |
N |
N |
0 |
10.227 |
-2.096 |
-0.258 |
8 |
C15 |
C |
C5 |
N |
N |
N |
0 |
8.987 |
-1.913 |
0.502 |
9 |
C16 |
C |
C6 |
N |
N |
N |
0 |
8.262 |
-0.663 |
0.0 |
10 |
C17 |
C |
C7 |
N |
N |
N |
0 |
6.968 |
-0.472 |
0.793 |
11 |
C19 |
C |
C9 |
N |
N |
N |
0 |
4.948 |
0.97 |
1.084 |
12 |
C20 |
C |
C10 |
N |
N |
N |
0 |
4.233 |
2.201 |
0.59 |
13 |
O2 |
O |
O2 |
N |
N |
N |
0 |
4.712 |
2.861 |
-0.308 |
14 |
N3 |
N |
N2 |
N |
N |
N |
0 |
3.062 |
2.569 |
1.146 |
15 |
C21 |
C |
C11 |
R |
N |
N |
0 |
2.367 |
3.766 |
0.666 |
16 |
C22 |
C |
C12 |
R |
N |
N |
0 |
1.508 |
3.406 |
-0.549 |
17 |
O3 |
O |
O3 |
N |
N |
N |
0 |
0.586 |
2.375 |
-0.191 |
18 |
P1 |
P |
P1 |
N |
N |
N |
0 |
0.043 |
1.282 |
-1.241 |
19 |
O4 |
O |
O4 |
N |
N |
N |
0 |
1.19 |
0.594 |
-1.874 |
20 |
O5 |
O |
O5 |
N |
N |
N |
0 |
-0.835 |
2.015 |
-2.374 |
21 |
O6 |
O |
O6 |
N |
N |
N |
0 |
-0.87 |
0.203 |
-0.468 |
22 |
P2 |
P |
P2 |
N |
N |
N |
0 |
-1.355 |
-1.295 |
-0.802 |
23 |
O7 |
O |
O7 |
N |
N |
N |
0 |
-1.702 |
-1.393 |
-2.238 |
24 |
O8 |
O |
O8 |
N |
N |
N |
0 |
-0.169 |
-2.33 |
-0.465 |
25 |
O9 |
O |
O9 |
N |
N |
N |
0 |
-2.648 |
-1.652 |
0.088 |
26 |
C23 |
C |
C13 |
N |
N |
N |
0 |
-3.377 |
-2.872 |
-0.053 |
27 |
C24 |
C |
C14 |
R |
N |
N |
0 |
-4.541 |
-2.888 |
0.94 |
28 |
O10 |
O |
O10 |
N |
N |
N |
0 |
-5.496 |
-1.872 |
0.591 |
29 |
C25 |
C |
C15 |
R |
N |
N |
0 |
-6.802 |
-2.386 |
0.931 |
30 |
N4 |
N |
N3 |
N |
N |
N |
0 |
-7.844 |
-1.682 |
0.18 |
31 |
C26 |
C |
C16 |
N |
N |
N |
0 |
-7.766 |
-1.609 |
-1.184 |
32 |
C27 |
C |
C17 |
N |
N |
N |
0 |
-8.727 |
-0.961 |
-1.876 |
33 |
C28 |
C |
C18 |
N |
N |
N |
0 |
-9.801 |
-0.367 |
-1.17 |
34 |
O11 |
O |
O11 |
N |
N |
N |
0 |
-10.68 |
0.223 |
-1.772 |
35 |
N5 |
N |
N4 |
N |
N |
N |
0 |
-9.842 |
-0.461 |
0.174 |
36 |
C29 |
C |
C19 |
N |
N |
N |
0 |
-8.873 |
-1.118 |
0.838 |
37 |
O12 |
O |
O12 |
N |
N |
N |
0 |
-8.926 |
-1.199 |
2.05 |
38 |
C30 |
C |
C20 |
R |
N |
N |
0 |
-6.727 |
-3.874 |
0.503 |
39 |
O13 |
O |
O13 |
N |
N |
N |
0 |
-7.657 |
-4.665 |
1.245 |
40 |
C31 |
C |
C21 |
S |
N |
N |
0 |
-5.27 |
-4.245 |
0.871 |
41 |
O14 |
O |
O14 |
N |
N |
N |
0 |
-5.226 |
-4.901 |
2.14 |
42 |
O15 |
O |
O15 |
N |
N |
N |
0 |
0.787 |
4.562 |
-0.98 |
43 |
C32 |
C |
C22 |
R |
N |
N |
0 |
-0.108 |
5.091 |
0.0 |
44 |
C33 |
C |
C23 |
N |
N |
N |
0 |
-0.842 |
6.302 |
-0.579 |
45 |
O16 |
O |
O16 |
N |
N |
N |
0 |
-1.673 |
5.882 |
-1.663 |
46 |
C34 |
C |
C24 |
S |
N |
N |
0 |
0.686 |
5.518 |
1.237 |
47 |
O17 |
O |
O17 |
N |
N |
N |
0 |
-0.213 |
5.995 |
2.241 |
48 |
C35 |
C |
C25 |
R |
N |
N |
0 |
1.465 |
4.314 |
1.776 |
49 |
O18 |
O |
O18 |
N |
N |
N |
0 |
2.266 |
4.722 |
2.886 |
50 |
H1 |
H |
H1 |
N |
N |
N |
0 |
14.846 |
-5.661 |
-0.703 |
51 |
H2 |
H |
H2 |
N |
N |
N |
0 |
14.093 |
-4.887 |
-2.118 |
52 |
H3 |
H |
H3 |
N |
N |
N |
0 |
14.97 |
-3.899 |
-0.925 |
53 |
H12 |
H |
H4 |
N |
N |
N |
0 |
12.394 |
-5.45 |
-0.402 |
54 |
H11 |
H |
H5 |
N |
N |
N |
0 |
13.271 |
-4.462 |
0.791 |
55 |
H14 |
H |
H6 |
N |
N |
N |
0 |
12.951 |
-2.458 |
-0.634 |
56 |
H13 |
H |
H7 |
N |
N |
N |
0 |
12.073 |
-3.446 |
-1.827 |
57 |
H15 |
H |
H8 |
N |
N |
N |
0 |
10.466 |
-1.466 |
-0.956 |
58 |
H17 |
H |
H9 |
N |
N |
N |
0 |
8.346 |
-2.784 |
0.366 |
59 |
H16 |
H |
H10 |
N |
N |
N |
0 |
9.224 |
-1.796 |
1.559 |
60 |
H19 |
H |
H11 |
N |
N |
N |
0 |
8.903 |
0.208 |
0.135 |
61 |
H18 |
H |
H12 |
N |
N |
N |
0 |
8.026 |
-0.78 |
-1.058 |
62 |
H21 |
H |
H13 |
N |
N |
N |
0 |
6.326 |
-1.343 |
0.658 |
63 |
H20 |
H |
H14 |
N |
N |
N |
0 |
7.204 |
-0.355 |
1.851 |
64 |
H23 |
H |
H15 |
N |
N |
N |
0 |
6.883 |
1.65 |
0.426 |
65 |
H22 |
H |
H16 |
N |
N |
N |
0 |
6.006 |
0.662 |
-0.766 |
66 |
H24 |
H |
H17 |
N |
N |
N |
0 |
4.307 |
0.099 |
0.949 |
67 |
H25 |
H |
H18 |
N |
N |
N |
0 |
5.184 |
1.087 |
2.142 |
68 |
H26 |
H |
H19 |
N |
N |
N |
0 |
2.679 |
2.042 |
1.865 |
69 |
H27 |
H |
H20 |
N |
N |
N |
0 |
3.099 |
4.523 |
0.383 |
70 |
H28 |
H |
H21 |
N |
N |
N |
0 |
2.15 |
3.056 |
-1.357 |
71 |
H4 |
H |
H22 |
N |
N |
N |
0 |
-1.606 |
2.487 |
-2.03 |
72 |
H5 |
H |
H23 |
N |
N |
N |
0 |
0.111 |
-2.32 |
0.461 |
73 |
H29 |
H |
H24 |
N |
N |
N |
0 |
-3.766 |
-2.948 |
-1.069 |
74 |
H30 |
H |
H25 |
N |
N |
N |
0 |
-2.717 |
-3.716 |
0.147 |
75 |
H31 |
H |
H26 |
N |
N |
N |
0 |
-4.169 |
-2.716 |
1.95 |
76 |
H32 |
H |
H27 |
N |
N |
N |
0 |
-6.98 |
-2.303 |
2.003 |
77 |
H33 |
H |
H28 |
N |
N |
N |
0 |
-6.938 |
-2.068 |
-1.705 |
78 |
H34 |
H |
H29 |
N |
N |
N |
0 |
-8.677 |
-0.895 |
-2.953 |
79 |
H35 |
H |
H30 |
N |
N |
N |
0 |
-10.575 |
-0.057 |
0.664 |
80 |
H36 |
H |
H31 |
N |
N |
N |
0 |
-6.897 |
-3.98 |
-0.568 |
81 |
H37 |
H |
H32 |
N |
N |
N |
0 |
-7.587 |
-5.615 |
1.079 |
82 |
H38 |
H |
H33 |
N |
N |
N |
0 |
-4.831 |
-4.877 |
0.1 |
83 |
H39 |
H |
H34 |
N |
N |
N |
0 |
-5.719 |
-5.733 |
2.17 |
84 |
H40 |
H |
H35 |
N |
N |
N |
0 |
-0.833 |
4.326 |
0.28 |
85 |
H41 |
H |
H36 |
N |
N |
N |
0 |
-1.458 |
6.758 |
0.196 |
86 |
H42 |
H |
H37 |
N |
N |
N |
0 |
-0.115 |
7.029 |
-0.94 |
87 |
H43 |
H |
H38 |
N |
N |
N |
0 |
-2.17 |
6.6 |
-2.079 |
88 |
H44 |
H |
H39 |
N |
N |
N |
0 |
1.383 |
6.312 |
0.966 |
89 |
H45 |
H |
H40 |
N |
N |
N |
0 |
-0.743 |
6.755 |
1.965 |
90 |
H46 |
H |
H41 |
N |
N |
N |
0 |
0.766 |
3.54 |
2.093 |
91 |
H47 |
H |
H42 |
N |
N |
N |
0 |
1.759 |
5.086 |
3.625 |
NJ5 : Chemical Bonds
Total Number of Bonds: 93
NJ5 : Used in PDB Entries
Total Number of PDB Entries: 1
Ligand Code |
PDB Entry ID |
Type |
Total |
Distinct |
NJ5 |
6tka ![Open in New Window](/pdbe-srv/pdbechem/images/newwin.png?_debugResources=y&n=1724253979912) |
Bound ligand
|
1 |
1 |
|