Chemical Components in the PDB

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NJ5 : Summary

Code

NJ5

One-letter code

X

Molecule name

[[(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

ProgramVersionName
OpenEye OEToolkits 2.0.7 [[(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

Formula

C25 H42 N4 O18 P2

Formal charge

0

Molecular weight

748.565 Da

SMILES

TypeProgramVersionDescriptor
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

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

MGZXRAPGBJHSCZ-HDEQREAESA-N
NJ5

wwPDB Information

Atom count

91 (49 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-11-29

Last modified at

2020-02-28

Status

Released

Obsoleted

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
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O4 P1 O P doub 1.48 N N
2 O18 C35 O C sing 1.43 N N
3 O17 C34 O C sing 1.43 N N
4 O5 P1 O P sing 1.61 N N
5 P1 O3 P O sing 1.61 N N
6 P1 O6 P O sing 1.61 N N
7 C35 C34 C C sing 1.53 N N
8 C35 C21 C C sing 1.53 N N
9 O13 C30 O C sing 1.43 N N
10 O3 C22 O C sing 1.43 N N
11 C19 C18 C C sing 1.53 N N
12 C19 C20 C C sing 1.51 N N
13 N3 C21 N C sing 1.47 N N
14 N3 C20 N C sing 1.35 N N
15 C30 C31 C C sing 1.55 N N
16 C30 C25 C C sing 1.55 N N
17 C27 C26 C C doub 1.35 N N
18 C27 C28 C C sing 1.42 N N
19 C34 C32 C C sing 1.53 N N
20 C26 N4 C N sing 1.37 N N
21 C21 C22 C C sing 1.53 N N
22 O9 C23 O C sing 1.43 N N
23 O9 P2 O P sing 1.61 N N
24 C18 C17 C C sing 1.53 N N
25 C20 O2 C O doub 1.21 N N
26 O11 C28 O C doub 1.22 N N
27 O6 P2 O P sing 1.61 N N
28 C28 N5 C N sing 1.35 N N
29 C31 O14 C O sing 1.43 N N
30 C31 C24 C C sing 1.54 N N
31 C32 O15 C O sing 1.43 N N
32 C32 C33 C C sing 1.53 N N
33 C22 O15 C O sing 1.43 N N
34 C23 C24 C C sing 1.53 N N
35 N4 C25 N C sing 1.46 N N
36 N4 C29 N C sing 1.35 N N
37 O7 P2 O P doub 1.48 N N
38 C17 C16 C C sing 1.53 N N
39 P2 O8 P O sing 1.61 N N
40 C25 O10 C O sing 1.44 N N
41 N5 C29 N C sing 1.35 N N
42 C24 O10 C O sing 1.44 N N
43 C33 O16 C O sing 1.43 N N
44 C29 O12 C O doub 1.22 N N
45 C16 C15 C C sing 1.53 N N
46 C15 N2 C N sing 1.47 N N
47 N2 C14 N C sing 1.35 N N
48 C14 O1 C O doub 1.21 N N
49 C14 C13 C C sing 1.51 N N
50 C13 C12 C C sing 1.53 N N
51 C12 C11 C C sing 1.53 N N
52 C11 H1 C H sing 1.09 N N
53 C11 H2 C H sing 1.09 N N
54 C11 H3 C H sing 1.09 N N
55 C12 H12 C H sing 1.09 N N
56 C12 H11 C H sing 1.09 N N
57 C13 H14 C H sing 1.09 N N
58 C13 H13 C H sing 1.09 N N
59 N2 H15 N H sing 0.97 N N
60 C15 H17 C H sing 1.09 N N
61 C15 H16 C H sing 1.09 N N
62 C16 H19 C H sing 1.09 N N
63 C16 H18 C H sing 1.09 N N
64 C17 H21 C H sing 1.09 N N
65 C17 H20 C H sing 1.09 N N
66 C18 H23 C H sing 1.09 N N
67 C18 H22 C H sing 1.09 N N
68 C19 H24 C H sing 1.09 N N
69 C19 H25 C H sing 1.09 N N
70 N3 H26 N H sing 0.97 N N
71 C21 H27 C H sing 1.09 N N
72 C22 H28 C H sing 1.09 N N
73 O5 H4 O H sing 0.97 N N
74 O8 H5 O H sing 0.97 N N
75 C23 H29 C H sing 1.09 N N
76 C23 H30 C H sing 1.09 N N
77 C24 H31 C H sing 1.09 N N
78 C25 H32 C H sing 1.09 N N
79 C26 H33 C H sing 1.08 N N
80 C27 H34 C H sing 1.08 N N
81 N5 H35 N H sing 0.97 N N
82 C30 H36 C H sing 1.09 N N
83 O13 H37 O H sing 0.97 N N
84 C31 H38 C H sing 1.09 N N
85 O14 H39 O H sing 0.97 N N
86 C32 H40 C H sing 1.09 N N
87 C33 H41 C H sing 1.09 N N
88 C33 H42 C H sing 1.09 N N
89 O16 H43 O H sing 0.97 N N
90 C34 H44 C H sing 1.09 N N
91 O17 H45 O H sing 0.97 N N
92 C35 H46 C H sing 1.09 N N
93 O18 H47 O H sing 0.97 N N



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 Bound ligand 1 1