Chemical Components in the PDB

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NHD : Summary

Code

NHD

One-letter code

X

Molecule name

NICOTINAMIDE PURIN-6-OL-DINUCLEOTIDE

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(3-aminocarbonylpyridin-1-ium-1-yl)-3,4-dihydroxy-oxolan-2-yl]methyl [[(2R,3S,4R,5R)-3,4-dihydroxy-5-(6-hydroxypurin-9-yl)oxolan-2-yl]methoxy-hydroxy-phosphoryl] phosphate

Formula

C21 H26 N6 O15 P2

Formal charge

0

Molecular weight

664.41 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.341 NC(=O)c1ccc[n+](c1)[CH]2O[CH](CO[P]([O-])(=O)O[P](O)(=O)OC[CH]3O[CH]([CH](O)[CH]3O)n4cnc5c(O)ncnc45)[CH](O)[CH]2O
SMILES OpenEye OEToolkits 1.5.0 c1cc(c[n+](c1)C2C(C(C(O2)COP(=O)([O-])OP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5O)O)O)O)O)C(=O)N
Canonical SMILES CACTVS 3.341 NC(=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)[C@@H]3O)n4cnc5c(O)ncnc45)[C@@H](O)[C@H]2O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(c[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)n4cnc5c4ncnc5O)O)O)O)O)C(=O)N

IUPAC InChI

InChI=1S/C21H26N6O15P2/c22-17(32)9-2-1-3-26(4-9)20-15(30)13(28)10(40-20)5-38-43(34,35)42-44(36,37)39-6-11-14(29)16(31)21(41-11)27-8-25-12-18(27)23-7-24-19(12)33/h1-4,7-8,10-11,13-16,20-21,28-31H,5-6H2,(H4-,22,23,24,32,33,34,35,36,37)/t10-,11-,13-,14-,15-,16-,20-,21-/m1/s1

IUPAC InChI key

DGVSIBCCYUVRNA-NNYOXOHSSA-N
NHD

wwPDB Information

Atom count

70 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



NHD : Atoms of Molecule

Total Number of Atoms: 70
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 PA P AP R N N 0 -0.966 -0.971 0.838
2 O1A O AO1 N N N 0 -0.36 -0.511 2.107
3 O2A O AO2 N N N 0 -1.677 -2.397 1.069
4 O5B O AO5* N N N 0 -2.062 0.101 0.347
5 C5B C AC5* N N N 0 -2.983 0.274 1.425
6 C4B C AC4* R N N 0 -4.057 1.287 1.022
7 O4B O AO4* N N N 0 -4.867 0.745 -0.035
8 C3B C AC3* S N N 0 -4.987 1.569 2.217
9 O3B O AO3* N N N 0 -4.952 2.953 2.571
10 C2B C AC2* R N N 0 -6.396 1.177 1.7
11 O2B O AO2* N N N 0 -7.378 2.118 2.135
12 C1B C AC1* R N N 0 -6.207 1.245 0.163
13 N9A N AN9 N Y N 0 -7.183 0.39 -0.518
14 C8A C AC8 N Y N 0 -7.011 -0.92 -0.854
15 N7A N AN7 N Y N 0 -8.078 -1.371 -1.447
16 C5A C AC5 N Y N 0 -9.0 -0.382 -1.53
17 C6A C AC6 N Y N 0 -10.299 -0.285 -2.051
18 O6A O AO6 N N N 0 -10.893 -1.353 -2.635
19 N1A N AN1 N Y N 0 -10.933 0.878 -1.958
20 C2A C AC2 N Y N 0 -10.363 1.925 -1.389
21 N3A N AN3 N Y N 0 -9.147 1.881 -0.887
22 C4A C AC4 N Y N 0 -8.438 0.759 -0.93
23 O3 O O3 N N N 0 0.181 -1.118 -0.282
24 PN P NP N N N 0 1.42 -1.871 0.417
25 O1N O NO1 N N N 0 1.14 -3.39 0.463
26 O2N O NO2 N N N -1 1.602 -1.338 1.855
27 O5D O NO5* N N N 0 2.761 -1.598 -0.431
28 C5D C NC5* N N N 0 3.839 -2.19 0.299
29 C4D C NC4* R N N 0 5.15 -1.965 -0.456
30 O4D O NO4* N N N 0 5.483 -0.56 -0.479
31 C3D C NC3* S N N 0 6.325 -2.637 0.289
32 C1D C NC1* R N N 0 6.901 -0.509 -0.747
33 O3D O NO3* N N N 0 6.625 -3.907 -0.291
34 C2D C NC2* R N N 0 7.505 -1.657 0.091
35 O2D O NO2* N N N 0 8.572 -2.294 -0.615
36 N1N N NN1 N Y N 1 7.454 0.779 -0.322
37 C2N C NC2 N Y N 0 8.397 1.342 -1.05
38 C3N C NC3 N Y N 0 8.951 2.565 -0.671
39 C7N C NC7 N N N 0 10.015 3.192 -1.483
40 O7N O NO7 N N N 0 10.417 2.64 -2.489
41 N7N N NN7 N N N 0 10.538 4.377 -1.11
42 C4N C NC4 N Y N 0 8.479 3.19 0.49
43 H51A H AH51 N N N 0 -3.454 -0.681 1.658
44 C5N C NC5 N Y N 0 7.483 2.561 1.215
45 C6N C NC6 N Y N 0 6.99 1.345 0.775
46 HOA2 H 2HOA N N N 0 -2.057 -2.661 0.22
47 H52A H AH52 N N N 0 -2.45 0.64 2.303
48 H4B H AH4* N N N 0 -3.587 2.213 0.69
49 H3B H AH3* N N N 0 -4.708 0.951 3.071
50 HO3A H AHO3 N N N 0 -5.596 3.077 3.281
51 H2B H AH2* N N N 0 -6.66 0.167 2.015
52 HO2A H AHO2 N N N 0 -7.448 2.026 3.095
53 H1B H AH1* N N N 0 -6.289 2.273 -0.189
54 H8A H AH8 N N N 0 -6.121 -1.499 -0.657
55 H6A H AH6 N N N 0 -11.363 -1.828 -1.937
56 H2A H AH2 N N N 0 -10.915 2.851 -1.335
57 H51N H NH51 N N N 0 3.66 -3.259 0.407
58 H52N H NH52 N N N 0 3.904 -1.731 1.285
59 H4D H NH4* N N N 0 5.074 -2.354 -1.472
60 H3D H NH3* N N N 0 6.092 -2.747 1.348
61 HO3N H NHO3 N N N 0 7.362 -4.278 0.213
62 H2D H NH2* N N N 0 7.856 -1.282 1.053
63 HO2N H NHO2 N N N 0 8.865 -3.036 -0.069
64 H1D H NH1* N N N 0 7.093 -0.672 -1.808
65 H2N H NH2 N N N 0 8.752 0.847 -1.942
66 H71N H NH71 N N N 0 11.236 4.789 -1.643
67 H72N H NH72 N N N 0 10.214 4.819 -0.309
68 H4N H NH4 N N N 0 8.883 4.139 0.811
69 H5N H NH5 N N N 0 7.095 3.013 2.115
70 H6N H NH6 N N N 0 6.212 0.852 1.339



NHD : Chemical Bonds

Total Number of Bonds: 74
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 O2A HOA2 O H sing 0.97 N N
6 O5B C5B O C sing 1.43 N N
7 C5B C4B C C sing 1.53 N N
8 C5B H51A C H sing 1.09 N N
9 C5B H52A C H sing 1.09 N N
10 C4B O4B C O sing 1.44 N N
11 C4B C3B C C sing 1.54 N N
12 C4B H4B C H sing 1.09 N N
13 O4B C1B O C sing 1.44 N N
14 C3B O3B C O sing 1.43 N N
15 C3B C2B C C sing 1.55 N N
16 C3B H3B C H sing 1.09 N N
17 O3B HO3A O H sing 0.97 N N
18 C2B O2B C O sing 1.43 N N
19 C2B C1B C C sing 1.55 N N
20 C2B H2B C H sing 1.09 N N
21 O2B HO2A O H sing 0.97 N N
22 C1B N9A C N sing 1.47 N N
23 C1B H1B C H sing 1.09 N N
24 N9A C8A N C sing 1.36 N Y
25 N9A C4A N C sing 1.37 N Y
26 C8A N7A C N doub 1.3 N Y
27 C8A H8A C H sing 1.08 N N
28 N7A C5A N C sing 1.35 N Y
29 C5A C6A C C sing 1.4 N Y
30 C5A C4A C C doub 1.41 N Y
31 C6A O6A C O sing 1.35 N N
32 C6A N1A C N doub 1.33 N Y
33 O6A H6A O H sing 0.97 N N
34 N1A C2A N C sing 1.32 N Y
35 C2A N3A C N doub 1.32 N Y
36 C2A H2A C H sing 1.08 N N
37 N3A C4A N C sing 1.33 N Y
38 O3 PN O P sing 1.61 N N
39 PN O1N P O doub 1.55 N N
40 PN O2N P O sing 1.54 N N
41 PN O5D P O sing 1.61 N N
42 O5D C5D O C sing 1.43 N N
43 C5D C4D C C sing 1.53 N N
44 C5D H51N C H sing 1.09 N N
45 C5D H52N C H sing 1.09 N N
46 C4D O4D C O sing 1.44 N N
47 C4D C3D C C sing 1.55 N N
48 C4D H4D C H sing 1.09 N N
49 O4D C1D O C sing 1.44 N N
50 C3D O3D C O sing 1.43 N N
51 C3D C2D C C sing 1.55 N N
52 C3D H3D C H sing 1.09 N N
53 O3D HO3N O H sing 0.97 N N
54 C2D O2D C O sing 1.43 N N
55 C2D C1D C C sing 1.54 N N
56 C2D H2D C H sing 1.09 N N
57 O2D HO2N O H sing 0.97 N N
58 C1D N1N C N sing 1.46 N N
59 C1D H1D C H sing 1.09 N N
60 N1N C2N N C sing 1.32 N Y
61 N1N C6N N C doub 1.32 N Y
62 C2N C3N C C doub 1.4 N Y
63 C2N H2N C H sing 1.08 N N
64 C3N C7N C C sing 1.48 N N
65 C3N C4N C C sing 1.4 N Y
66 C7N O7N C O doub 1.22 N N
67 C7N N7N C N sing 1.35 N N
68 N7N H71N N H sing 0.97 N N
69 N7N H72N N H sing 0.97 N N
70 C4N C5N C C doub 1.38 N Y
71 C4N H4N C H sing 1.08 N N
72 C5N C6N C C sing 1.38 N Y
73 C5N H5N C H sing 1.08 N N
74 C6N H6N C H sing 1.08 N N



NHD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
NHD 1drw Open in New Window Bound ligand 1 1