Chemical Components in the PDB

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8OD : Summary

Code

8OD

One-letter code

X

Molecule name

[(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen phosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 8-oxoadenosine 5'-(trihydrogen diphosphate)
OpenEye OEToolkits 1.7.0 [(2R,3S,4R,5R)-5-(6-azanyl-8-oxo-7H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl phosphono hydrogen phosphate

Formula

C10 H15 N5 O11 P2

Formal charge

0

Molecular weight

443.201 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OP(=O)(O)OCC3OC(N2C(=O)Nc1c(ncnc12)N)C(O)C3O
SMILES CACTVS 3.370 Nc1ncnc2N([CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O)C(=O)Nc12
SMILES OpenEye OEToolkits 1.7.0 c1nc(c2c(n1)N(C(=O)N2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
Canonical SMILES CACTVS 3.370 Nc1ncnc2N([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O)C(=O)Nc12
Canonical SMILES OpenEye OEToolkits 1.7.0 c1nc(c2c(n1)N(C(=O)N2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N

IUPAC InChI

InChI=1S/C10H15N5O11P2/c11-7-4-8(13-2-12-7)15(10(18)14-4)9-6(17)5(16)3(25-9)1-24-28(22,23)26-27(19,20)21/h2-3,5-6,9,16-17H,1H2,(H,14,18)(H,22,23)(H2,11,12,13)(H2,19,20,21)/t3-,5-,6-,9-/m1/s1

IUPAC InChI key

RKHXUJRVBUXHAN-UUOKFMHZSA-N
8OD

wwPDB Information

Atom count

43 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-06-15

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



8OD : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 -6.277 1.975 1.133
2 C2 C C2 N Y N 0 -5.831 1.0 1.901
3 N3 N N3 N Y N 0 -4.764 0.292 1.59
4 C4 C C4 N Y N 0 -4.089 0.539 0.473
5 C5 C C5 N Y N 0 -4.527 1.563 -0.37
6 C6 C C6 N Y N 0 -5.659 2.289 -0.004
7 N6 N N6 N N N 0 -6.133 3.315 -0.809
8 N7 N N7 N N N 0 -3.648 1.602 -1.449
9 C8 C C8 N N N 0 -2.719 0.643 -1.268
10 O8 O O8 N N N 0 -1.799 0.404 -2.027
11 N9 N N9 N N N 0 -2.964 -0.011 -0.116
12 PA P PA N N N 0 3.59 -0.621 -0.274
13 PB P PB N N N 0 5.43 1.601 0.405
14 C1' C C1' R N N 0 -2.172 -1.118 0.424
15 O2' O O2' N N N 0 -3.403 -3.151 -0.189
16 O1A O O1A N N N 0 3.463 -0.139 -1.668
17 O1B O O1B N N N 0 5.967 2.124 1.829
18 C2' C C2' R N N 0 -2.259 -2.355 -0.505
19 O2A O O2A N N N 0 4.528 -1.929 -0.242
20 O2B O O2B N N N 0 6.539 0.957 -0.335
21 C3' C C3' S N N 0 -0.951 -3.11 -0.164
22 O3' O O3' N N N 0 -1.206 -4.153 0.779
23 O3A O O3A N N N 0 4.247 0.534 0.635
24 O3B O O3B N N N 0 4.869 2.847 -0.447
25 C4' C C4' R N N 0 -0.044 -2.031 0.459
26 O4' O O4' N N N 0 -0.766 -0.789 0.416
27 C5' C C5' N N N 0 1.25 -1.909 -0.349
28 O5' O O5' N N N 0 2.132 -0.992 0.301
29 H2 H H2 N N N 0 -6.358 0.775 2.816
30 HN6 H HN6 N N N 0 -6.922 3.813 -0.544
31 HN6A H HN6A N N N 0 -5.675 3.534 -1.635
32 HN7 H HN7 N N N 0 -3.697 2.213 -2.201
33 H1' H H1' N N N 0 -2.503 -1.37 1.432
34 HO1B H HO1B N N N 0 6.682 2.772 1.767
35 H2' H H2' N N N 0 -2.273 -2.055 -1.553
36 HO2' H HO2' N N N 0 -3.501 -3.937 -0.744
37 HO2A H HO2A N N N 0 4.655 -2.3 0.642
38 H3' H H3' N N N 0 -0.498 -3.516 -1.068
39 HO3' H HO3' N N N 0 -1.819 -4.83 0.459
40 HO3B H HO3B N N N 0 4.139 3.318 -0.022
41 H4' H H4' N N N 0 0.185 -2.291 1.492
42 H5' H H5' N N N 0 1.728 -2.886 -0.419
43 H5'A H H5'A N N N 0 1.02 -1.544 -1.35



8OD : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C2 N C doub 1.32 N Y
2 N1 C6 N C sing 1.33 N Y
3 C2 N3 C N sing 1.32 N Y
4 N3 C4 N C doub 1.33 N Y
5 C4 C5 C C sing 1.4 N Y
6 C4 N9 C N sing 1.38 N N
7 C5 C6 C C doub 1.39 N Y
8 C5 N7 C N sing 1.39 N N
9 C6 N6 C N sing 1.39 N N
10 N7 C8 N C sing 1.35 N N
11 C8 O8 C O doub 1.22 N N
12 C8 N9 C N sing 1.35 N N
13 N9 C1' N C sing 1.46 N N
14 PA O1A P O doub 1.48 N N
15 PA O2A P O sing 1.61 N N
16 PA O3A P O sing 1.61 N N
17 PA O5' P O sing 1.61 N N
18 PB O1B P O sing 1.61 N N
19 PB O2B P O doub 1.48 N N
20 PB O3A P O sing 1.61 N N
21 PB O3B P O sing 1.61 N N
22 C1' C2' C C sing 1.55 N N
23 C1' O4' C O sing 1.44 N N
24 C2' O2' C O sing 1.43 N N
25 C2' C3' C C sing 1.55 N N
26 C3' O3' C O sing 1.43 N N
27 C3' C4' C C sing 1.54 N N
28 C4' O4' C O sing 1.44 N N
29 C4' C5' C C sing 1.53 N N
30 C5' O5' C O sing 1.43 N N
31 C2 H2 C H sing 1.08 N N
32 N6 HN6 N H sing 0.97 N N
33 N6 HN6A N H sing 0.97 N N
34 N7 HN7 N H sing 0.97 N N
35 C1' H1' C H sing 1.09 N N
36 O1B HO1B O H sing 0.97 N N
37 C2' H2' C H sing 1.09 N N
38 O2' HO2' O H sing 0.97 N N
39 O2A HO2A O H sing 0.97 N N
40 C3' H3' C H sing 1.09 N N
41 O3' HO3' O H sing 0.97 N N
42 O3B HO3B O H sing 0.97 N N
43 C4' H4' C H sing 1.09 N N
44 C5' H5' C H sing 1.09 N N
45 C5' H5'A C H sing 1.09 N N



8OD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
8OD 3nbf Open in New Window Bound ligand 6 1