Chemical Components in the PDB

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NA0 : Summary

Code

NA0

One-letter code

X

Molecule name

3-ACETYLPYRIDINE ADENINE DINUCLEOTIDE PHOSPHATE

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.6.1 [[(2S,3R,4R,5R)-5-(6-aminopurin-9-yl)-3-hydroxy-4-phosphonooxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl] [(2S,3S,4R,5R)-5-(3-ethanoylpyridin-1-ium-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphate

Formula

C22 H29 N6 O17 P3

Formal charge

0

Molecular weight

742.417 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.352 CC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O[P](O)(O)=O)[CH]3O)n4cnc5c(N)ncnc45)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.6.1 CC(=O)c1ccc[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O
Canonical SMILES CACTVS 3.352 CC(=O)c1ccc[n+](c1)[C@@H]2O[C@@H](CO[P]([O-])(=O)O[P](O)(=O)OC[C@@H]3O[C@H]([C@H](O[P](O)(O)=O)[C@@H]3O)n4cnc5c(N)ncnc45)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.6.1 CC(=O)c1ccc[n+](c1)[C@H]2[C@@H]([C@@H]([C@@H](O2)CO[P@@](=O)([O-])O[P@](=O)(O)OC[C@H]3[C@H]([C@H]([C@@H](O3)n4cnc5c4ncnc5N)OP(=O)(O)O)O)O)O

IUPAC InChI

InChI=1S/C22H29N6O17P3/c1-10(29)11-3-2-4-27(5-11)21-17(32)15(30)12(42-21)6-40-47(36,37)45-48(38,39)41-7-13-16(31)18(44-46(33,34)35)22(43-13)28-9-26-14-19(23)24-8-25-20(14)28/h2-5,8-9,12-13,15-18,21-22,30-32H,6-7H2,1H3,(H5-,23,24,25,33,34,35,36,37,38,39)/t12-,13-,15+,16+,17+,18+,21+,22+/m0/s1

IUPAC InChI key

CWZSJEPJRFQEBR-SIEFPTHMSA-N
NA0

wwPDB Information

Atom count

77 (48 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-07-21

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



NA0 : Atoms of Molecule

Total Number of Atoms: 77
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 PN P PN N N N 0 -2.613 -3.206 -0.835
2 O1N O O1N N N N 0 -3.186 -4.322 0.066
3 O2N O O2N N N N -1 -2.274 -3.79 -2.225
4 O5D O O5D N N N 0 -3.705 -2.034 -0.998
5 C5D C C5D N N N 0 -5.035 -2.268 -1.466
6 C4B C C4B S N N 0 3.344 -1.186 1.116
7 O4B O O4B N N N 0 3.565 -0.747 -0.234
8 C3B C C3B R N N 0 4.756 -1.478 1.682
9 O3B O O3B N N N 0 5.217 -2.769 1.278
10 C2B C C2B R N N 0 5.584 -0.351 1.006
11 O2B O O2B N N N 0 6.947 -0.749 0.843
12 C1B C C1B R N N 0 4.886 -0.209 -0.364
13 N9A N N9A N Y N 0 4.812 1.205 -0.739
14 C8A C C8A N Y N 0 3.761 2.045 -0.517
15 N7A N N7A N Y N 0 4.034 3.23 -0.98
16 C5A C C5A N Y N 0 5.274 3.227 -1.526
17 C6A C C6A N Y N 0 6.077 4.19 -2.159
18 N6A N N6A N N N 0 5.625 5.487 -2.332
19 N1A N N1A N Y N 0 7.283 3.828 -2.586
20 C2A C C2A N Y N 0 7.723 2.593 -2.425
21 N3A N N3A N Y N 0 7.005 1.658 -1.838
22 C4A C C4A N Y N 0 5.79 1.929 -1.373
23 O3 O O3 N N N 0 -1.278 -2.606 -0.165
24 PA P PA N N N 0 0.018 -3.264 0.528
25 O2A O O2A N N N 0 -0.371 -3.797 1.997
26 O1A O O1A N N N 0 0.498 -4.395 -0.296
27 O5B O O5B N N N 0 1.181 -2.157 0.65
28 C5B C C5B N N N 0 2.494 -2.458 1.128
29 C4D C C4D S N N 0 -5.804 -0.946 -1.5
30 O4D O O4D N N N 0 -5.996 -0.447 -0.167
31 C3D C C3D S N N 0 -7.233 -1.169 -2.057
32 O3D O O3D N N N 0 -7.772 -2.414 -1.607
33 C2D C C2D R N N 0 -7.988 0.03 -1.422
34 O2D O O2D N N N 0 -9.372 -0.276 -1.246
35 C1D C C1D R N N 0 -7.28 0.177 -0.057
36 N1N N N1N N Y N 1 -7.118 1.596 0.268
37 C2N C C2N N Y N 0 -7.959 2.159 1.11
38 C3N C C3N N Y N 0 -7.832 3.511 1.443
39 C7N C C7N N N N 0 -8.771 4.141 2.384
40 O7N O O7N N N N 0 -9.665 3.487 2.879
41 C4N C C4N N Y N 0 -6.794 4.256 0.863
42 C5N C C5N N Y N 0 -5.94 3.615 -0.015
43 C6N C C6N N Y N 0 -6.13 2.271 -0.287
44 P2B P P2B N N N 0 8.18 0.066 1.481
45 O2X O O2X N N N 0 9.567 -0.588 0.989
46 O1X O O1X N N N 0 8.118 1.478 1.043
47 O3X O O3X N N N 0 8.095 -0.002 3.087
48 CAA C CAA N N N 0 -8.623 5.6 2.733
49 H5B1 H H5B1 N N N 0 2.952 -3.208 0.484
50 H5B2 H H5B2 N N N 0 2.43 -2.842 2.146
51 H4B H H4B N N N 0 2.859 -0.4 1.695
52 H3B H H3B N N N 0 4.772 -1.38 2.768
53 H1B H H1B N N N 0 5.439 -0.765 -1.12
54 HA H HA N N N 0 4.665 -3.499 1.589
55 H2B H H2B N N N 0 5.518 0.575 1.577
56 H8A H H8A N N N 0 2.838 1.767 -0.03
57 H6A1 H H6A1 N N N 0 4.744 5.739 -2.016
58 H6A2 H H6A2 N N N 0 6.189 6.143 -2.771
59 H2A H H2A N N N 0 8.708 2.341 -2.787
60 H5D1 H H5D1 N N N 0 -4.997 -2.692 -2.47
61 H5D2 H H5D2 N N N 0 -5.538 -2.965 -0.796
62 H4D H H4D N N N 0 -5.271 -0.214 -2.105
63 H3D H H3D N N N 0 -7.244 -1.11 -3.145
64 H1D H H1D N N N 0 -7.866 -0.317 0.718
65 HB H HB N N N 0 -8.665 -2.596 -1.932
66 H2D H H2D N N N 0 -7.864 0.929 -2.025
67 HC H HC N N N 0 -9.841 -0.464 -2.071
68 H4N H H4N N N N 0 -6.667 5.302 1.097
69 HD H HD N N N 0 -8.753 1.571 1.548
70 H6N H H6N N N N 0 -5.46 1.768 -0.969
71 H5N H H5N N N N 0 -5.129 4.156 -0.48
72 H2X H H2X N N N 0 10.355 -0.147 1.336
73 HAA1 H HAA1 N N N 0 -9.204 6.201 2.035
74 HAA2 H HAA2 N N N 0 -8.985 5.769 3.747
75 HAA3 H HAA3 N N N 0 -7.573 5.883 2.67
76 H21 H H21 N N N 0 -0.695 -3.108 2.593
77 H3X H H3X N N N 0 8.13 -0.9 3.445



NA0 : Chemical Bonds

Total Number of Bonds: 81
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 PA O1A P O doub 1.48 N N
2 PA O2A P O sing 1.61 N N
3 PA O5B P O sing 1.61 N N
4 PA O3 P O sing 1.61 N N
5 O5B C5B O C sing 1.43 N N
6 C5B C4B C C sing 1.53 N N
7 C4B O4B C O sing 1.44 N N
8 C4B C3B C C sing 1.55 N N
9 O4B C1B O C sing 1.43 N N
10 C3B O3B C O sing 1.43 N N
11 C3B C2B C C sing 1.55 N N
12 C2B O2B C O sing 1.43 N N
13 C2B C1B C C sing 1.54 N N
14 O2B P2B O P sing 1.61 N N
15 C1B N9A C N sing 1.46 N N
16 N9A C8A N C sing 1.36 N Y
17 N9A C4A N C sing 1.37 N Y
18 C8A N7A C N doub 1.3 N Y
19 N7A C5A N C sing 1.35 N Y
20 C5A C6A C C doub 1.4 N Y
21 C5A C4A C C sing 1.41 N Y
22 C6A N6A C N sing 1.38 N N
23 C6A N1A C N sing 1.33 N Y
24 N1A C2A N C doub 1.32 N Y
25 C2A N3A C N sing 1.32 N Y
26 N3A C4A N C doub 1.33 N Y
27 O3 PN O P sing 1.61 N N
28 PN O1N P O doub 1.54 N N
29 PN O2N P O sing 1.55 N N
30 PN O5D P O sing 1.61 N N
31 O5D C5D O C sing 1.43 N N
32 C5D C4D C C sing 1.53 N N
33 C4D O4D C O sing 1.44 N N
34 C4D C3D C C sing 1.55 N N
35 O4D C1D O C sing 1.43 N N
36 C3D O3D C O sing 1.43 N N
37 C3D C2D C C sing 1.55 N N
38 C2D O2D C O sing 1.43 N N
39 C2D C1D C C sing 1.54 N N
40 C1D N1N C N sing 1.46 N N
41 N1N C2N N C sing 1.32 N Y
42 N1N C6N N C doub 1.32 N Y
43 C2N C3N C C doub 1.4 N Y
44 C3N C7N C C sing 1.47 N N
45 C3N C4N C C sing 1.4 N Y
46 C7N O7N C O doub 1.21 N N
47 C7N CAA C C sing 1.51 N N
48 C4N C5N C C doub 1.38 N Y
49 C5N C6N C C sing 1.38 N Y
50 P2B O1X P O doub 1.48 N N
51 P2B O2X P O sing 1.61 N N
52 P2B O3X P O sing 1.61 N N
53 C5B H5B1 C H sing 1.09 N N
54 C5B H5B2 C H sing 1.09 N N
55 C4B H4B C H sing 1.09 N N
56 C3B H3B C H sing 1.09 N N
57 C1B H1B C H sing 1.09 N N
58 O3B HA O H sing 0.97 N N
59 C2B H2B C H sing 1.09 N N
60 C8A H8A C H sing 1.08 N N
61 N6A H6A1 N H sing 0.97 N N
62 N6A H6A2 N H sing 0.97 N N
63 C2A H2A C H sing 1.08 N N
64 C5D H5D1 C H sing 1.09 N N
65 C5D H5D2 C H sing 1.09 N N
66 C4D H4D C H sing 1.09 N N
67 C3D H3D C H sing 1.09 N N
68 C1D H1D C H sing 1.09 N N
69 O3D HB O H sing 0.97 N N
70 C2D H2D C H sing 1.09 N N
71 O2D HC O H sing 0.97 N N
72 C2N HD C H sing 1.08 N N
73 C6N H6N C H sing 1.08 N N
74 C4N H4N C H sing 1.08 N N
75 C5N H5N C H sing 1.08 N N
76 O2X H2X O H sing 0.97 N N
77 O3X H3X O H sing 0.97 N N
78 CAA HAA1 C H sing 1.09 N N
79 CAA HAA2 C H sing 1.09 N N
80 CAA HAA3 C H sing 1.09 N N
81 O2A H21 O H sing 0.97 N N



NA0 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
NA0 2xlt Open in New Window Bound ligand 4 1