Chemical Components in the PDB

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OIG : Summary

Code

OIG

One-letter code

X

Molecule name

beta-ethyl-adenosine diphosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 3.1.0.0 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethyl hydrogen phosphate

Formula

C12 H19 N5 O10 P2

Formal charge

0

Molecular weight

455.254 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCO[P](O)(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 3.1.0.0 CCOP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Canonical SMILES CACTVS 3.385 CCO[P](O)(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 3.1.0.0 CCOP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O

IUPAC InChI

InChI=1S/C12H19N5O10P2/c1-2-24-28(20,21)27-29(22,23)25-3-6-8(18)9(19)12(26-6)17-5-16-7-10(13)14-4-15-11(7)17/h4-6,8-9,12,18-19H,2-3H2,1H3,(H,20,21)(H,22,23)(H2,13,14,15)/t6-,8-,9-,12-/m1/s1

IUPAC InChI key

OBBAXRNSCNGYQO-WOUKDFQISA-N
OIG

wwPDB Information

Atom count

48 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-09-07

Last modified at

2024-03-15

Status

Released

Obsoleted

Not Assigned



OIG : Atoms of Molecule

Total Number of Atoms: 48
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4' C C1 R N N 0 -0.689 1.885 -0.506
2 C1' C C2 R N N 0 -2.727 0.79 -0.604
3 C8 C C3 N Y N 0 -3.035 -1.224 0.885
4 C6 C C4 N Y N 0 -6.361 -2.36 0.327
5 C2' C C5 R N N 0 -3.02 2.096 0.177
6 C3' C C6 S N N 0 -1.745 2.931 -0.099
7 C05 C C7 N N N 0 6.997 -2.447 -0.945
8 C06 C C8 N N N 0 6.902 -3.705 -1.81
9 C5' C C9 N N N 0 0.508 1.959 0.443
10 C5 C C10 N Y N 0 -5.079 -1.795 0.44
11 C2 C C11 N Y N 0 -6.898 -0.744 -1.232
12 C4 C C12 N Y N 0 -4.78 -0.669 -0.345
13 N9 N N1 N Y N 0 -3.486 -0.329 -0.04
14 N7 N N2 N Y N 0 -3.971 -2.085 1.162
15 N6 N N3 N N N 0 -6.711 -3.475 1.068
16 N1 N N4 N Y N 0 -7.23 -1.798 -0.507
17 N3 N N5 N Y N 0 -5.712 -0.18 -1.157
18 O1B O O1 N N N 0 5.878 -0.653 1.357
19 O2B O O2 N N N 0 6.277 0.744 -0.707
20 O3B O O3 N N N 0 5.715 -1.819 -0.875
21 O3A O O4 N N N 0 3.874 -0.12 -0.08
22 O1A O O5 N N N 0 3.591 2.188 0.902
23 O2A O O6 N N N 0 2.666 0.248 2.226
24 O5' O O7 N N N 0 1.523 1.056 0.0
25 O4' O O8 N N N 0 -1.31 0.592 -0.412
26 O2' O O9 N N N 0 -4.181 2.75 -0.34
27 O3' O O10 N N N 0 -1.973 3.854 -1.167
28 PB P P1 N N N 0 5.445 -0.466 -0.045
29 PA P P2 N N N 0 2.928 0.872 0.765
30 H4' H H1 N N N 0 -0.362 2.066 -1.53
31 H1' H H2 N N N 0 -2.957 0.916 -1.663
32 H8 H H3 N N N 0 -2.047 -1.221 1.319
33 H2' H H4 N N N 0 -3.13 1.896 1.242
34 H3' H H5 N N N 0 -1.433 3.459 0.802
35 H6 H H6 N N N 0 7.322 -2.72 0.059
36 H7 H H7 N N N 0 7.717 -1.757 -1.384
37 H1 H H8 N N N 0 6.577 -3.432 -2.814
38 H9 H H9 N N N 0 7.88 -4.184 -1.863
39 H10 H H10 N N N 0 6.183 -4.396 -1.37
40 H5'1 H H11 N N N 0 0.903 2.974 0.452
41 H5'2 H H12 N N N 0 0.191 1.683 1.449
42 H2 H H13 N N N 0 -7.635 -0.319 -1.898
43 HN61 H H14 N N N 0 -6.069 -3.876 1.673
44 HN62 H H15 N N N 0 -7.599 -3.856 0.981
45 HOB2 H H16 N N N 0 6.044 0.923 -1.628
46 HOA2 H H17 N N N 0 2.233 -0.616 2.212
47 HO2' H H18 N N N 0 -4.404 3.573 0.117
48 HO3' H H19 N N N 0 -2.63 4.535 -0.965



OIG : Chemical Bonds

Total Number of Bonds: 50
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3' C3' O C sing 1.43 N N
2 O2' C2' O C sing 1.43 N N
3 C3' C4' C C sing 1.54 N N
4 C3' C2' C C sing 1.55 N N
5 C4' O4' C O sing 1.44 N N
6 C4' C5' C C sing 1.53 N N
7 C1' C2' C C sing 1.55 N N
8 C1' O4' C O sing 1.44 N N
9 C1' N9 C N sing 1.47 N N
10 N3 C2 N C doub 1.32 N Y
11 N3 C4 N C sing 1.33 N Y
12 C2 N1 C N sing 1.32 N Y
13 C4 N9 C N sing 1.37 N Y
14 C4 C5 C C doub 1.4 N Y
15 N9 C8 N C sing 1.36 N Y
16 C5' O5' C O sing 1.43 N N
17 N1 C6 N C doub 1.33 N Y
18 O5' PA O P sing 1.61 N N
19 C5 C6 C C sing 1.41 N Y
20 C5 N7 C N sing 1.35 N Y
21 C8 N7 C N doub 1.3 N Y
22 C6 N6 C N sing 1.38 N N
23 O1B PB O P doub 1.48 N N
24 O2B PB O P sing 1.61 N N
25 PA O3A P O sing 1.61 N N
26 PA O1A P O doub 1.48 N N
27 PA O2A P O sing 1.61 N N
28 PB O3A P O sing 1.61 N N
29 PB O3B P O sing 1.61 N N
30 O3B C05 O C sing 1.43 N N
31 C05 C06 C C sing 1.53 N N
32 C4' H4' C H sing 1.09 N N
33 C1' H1' C H sing 1.09 N N
34 C8 H8 C H sing 1.08 N N
35 C2' H2' C H sing 1.09 N N
36 C3' H3' C H sing 1.09 N N
37 C05 H6 C H sing 1.09 N N
38 C05 H7 C H sing 1.09 N N
39 C06 H1 C H sing 1.09 N N
40 C06 H9 C H sing 1.09 N N
41 C06 H10 C H sing 1.09 N N
42 C5' H5'1 C H sing 1.09 N N
43 C5' H5'2 C H sing 1.09 N N
44 C2 H2 C H sing 1.08 N N
45 N6 HN61 N H sing 0.97 N N
46 N6 HN62 N H sing 0.97 N N
47 O2B HOB2 O H sing 0.97 N N
48 O2A HOA2 O H sing 0.97 N N
49 O2' HO2' O H sing 0.97 N N
50 O3' HO3' O H sing 0.97 N N



OIG : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
OIG 8azo Open in New Window Bound ligand 2 1