Chemical Components in the PDB

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OI6 : Summary

Code

OI6

One-letter code

X

Molecule name

8-bromoadenosine 5'-diphosphoribose

Systematic names

ProgramVersionName
OpenEye OEToolkits 3.1.0.0 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-azanyl-8-bromanyl-purin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{R},5~{R})-3,4,5-tris(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate

Formula

C15 H22 Br N5 O14 P2

Formal charge

0

Molecular weight

638.212 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1ncnc2n([CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH](O)[CH](O)[CH]4O)[CH](O)[CH]3O)c(Br)nc12
SMILES OpenEye OEToolkits 3.1.0.0 c1nc(c2c(n1)n(c(n2)Br)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)O)O)O)O)O)N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n([C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)OC[C@H]4O[C@@H](O)[C@H](O)[C@@H]4O)[C@@H](O)[C@H]3O)c(Br)nc12
Canonical SMILES OpenEye OEToolkits 3.1.0.0 c1nc(c2c(n1)n(c(n2)Br)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)OP(=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)O)O)O)O)O)N

IUPAC InChI

InChI=1S/C15H22BrN5O14P2/c16-15-20-6-11(17)18-3-19-12(6)21(15)13-9(24)7(22)4(33-13)1-31-36(27,28)35-37(29,30)32-2-5-8(23)10(25)14(26)34-5/h3-5,7-10,13-14,22-26H,1-2H2,(H,27,28)(H,29,30)(H2,17,18,19)/t4-,5-,7-,8-,9-,10-,13-,14-/m1/s1

IUPAC InChI key

DPZGAPGUTMHLAW-AIKIOGRUSA-N
OI6

wwPDB Information

Atom count

59 (37 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



OI6 : Atoms of Molecule

Total Number of Atoms: 59
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 2.276 -1.668 -1.417
2 C1' C C2 R N N 0 3.872 -0.026 -1.251
3 C2 C C3 N Y N 0 6.199 3.783 -1.719
4 C3D C C4 S N N 0 -8.029 1.576 0.828
5 C4D C C5 R N N 0 -6.562 1.357 0.407
6 C5D C C6 N N N 0 -6.205 -0.126 0.521
7 C5' C C7 N N N 0 1.303 -2.534 -0.614
8 C4 C C8 N Y N 0 5.263 1.994 -0.623
9 C6 C C9 N Y N 0 6.532 3.667 0.562
10 C5 C C10 N Y N 0 5.785 2.477 0.589
11 C8 C C11 N Y N 0 4.706 0.648 1.034
12 C2' C C12 R N N 0 4.683 -1.312 -1.523
13 C3' C C13 S N N 0 3.609 -2.417 -1.634
14 C1D C C14 R N N 0 -7.464 2.78 -1.181
15 C2D C C15 R N N 0 -8.689 2.214 -0.419
16 N9 N N1 N Y N 0 4.588 0.84 -0.311
17 N3 N N2 N Y N 0 5.493 2.673 -1.742
18 N1 N N3 N Y N 0 6.71 4.277 -0.605
19 N6 N N4 N N N 0 7.071 4.191 1.724
20 N7 N N5 N Y N 0 5.409 1.61 1.56
21 O3D O O1 N N N 0 -8.102 2.465 1.944
22 O5D O O2 N N N 0 -4.814 -0.303 0.242
23 O1B O O3 N N N 0 -4.323 -2.385 1.582
24 O2B O O4 N N N 0 -4.695 -2.669 -0.898
25 O3A O O5 N N N 0 -2.509 -1.55 0.039
26 O1A O O6 N N N 0 -1.514 -3.848 -0.283
27 O2A O O7 N N N 0 -0.891 -2.605 1.823
28 O5' O O8 N N N 0 0.039 -1.873 -0.525
29 O4' O O9 N N N 0 2.634 -0.487 -0.667
30 O2' O O10 N N N 0 5.411 -1.196 -2.747
31 O3' O O11 N N N 0 3.641 -3.017 -2.931
32 O4D O O12 N N N 0 -6.441 1.786 -0.959
33 O1D O O13 N N N 0 -7.753 2.902 -2.576
34 O2D O O14 N N N 0 -9.584 3.263 -0.041
35 PB P P1 N N N 0 -4.09 -1.741 0.27
36 PA P P2 N N N 0 -1.225 -2.499 0.252
37 BR28 BR BR1 N N N 0 3.958 -0.8 1.993
38 H'4 H H1 N N N 0 1.835 -1.392 -2.375
39 H'1 H H3 N N N 0 3.679 0.505 -2.183
40 H2 H H4 N N N 0 6.372 4.309 -2.647
41 HR'3 H H5 N N N 0 -8.504 0.624 1.066
42 HR'4 H H6 N N N 0 -5.903 1.947 1.044
43 H5R1 H H8 N N N 0 -6.42 -0.476 1.53
44 H5R2 H H9 N N N 0 -6.794 -0.698 -0.196
45 H5'1 H H10 N N N 0 1.175 -3.495 -1.113
46 H5'2 H H11 N N N 0 1.701 -2.695 0.387
47 H'2 H H12 N N N 0 5.359 -1.519 -0.693
48 H'3 H H13 N N N 0 3.754 -3.171 -0.86
49 HR'2 H H14 N N N 0 -9.205 1.461 -1.015
50 H61 H H15 N N N 0 6.934 3.737 2.57
51 H62 H H16 N N N 0 7.585 5.013 1.692
52 HOR3 H H17 N N N 0 -9.003 2.639 2.25
53 HOB2 H H18 N N N 0 -4.578 -2.308 -1.787
54 HOA2 H H19 N N N 0 -0.691 -1.756 2.241
55 HO'2 H H21 N N N 0 5.939 -1.976 -2.966
56 HO'3 H H22 N N N 0 4.456 -3.501 -3.12
57 HOR1 H H24 N N N 0 -7.019 3.252 -3.1
58 HR'1 H H2 N N N 0 -7.163 3.741 -0.765
59 HOR2 H H25 N N N 0 -10.022 3.693 -0.787



OI6 : Chemical Bonds

Total Number of Bonds: 62
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4' C5' C C sing 1.53 N N
2 C4' C3' C C sing 1.54 N N
3 C1' C2' C C sing 1.54 N N
4 C1' N9 C N sing 1.46 N N
5 C1' O4' C O sing 1.44 N N
6 C2 N3 C N doub 1.32 N Y
7 C2 N1 C N sing 1.32 N Y
8 C3D C4D C C sing 1.54 N N
9 C3D C2D C C sing 1.55 N N
10 C3D O3D C O sing 1.43 N N
11 C4D C5D C C sing 1.53 N N
12 C5D O5D C O sing 1.43 N N
13 C5' O5' C O sing 1.43 N N
14 C4 C5 C C doub 1.41 N Y
15 C4 N9 C N sing 1.37 N Y
16 C4 N3 C N sing 1.33 N Y
17 C6 C5 C C sing 1.41 N Y
18 C6 N1 C N doub 1.33 N Y
19 C6 N6 C N sing 1.38 N N
20 C5 N7 C N sing 1.35 N Y
21 C8 N9 C N sing 1.36 N Y
22 C8 N7 C N doub 1.3 N Y
23 C8 BR28 C BR sing 1.89 N N
24 C2' C3' C C sing 1.54 N N
25 C2' O2' C O sing 1.43 N N
26 C3' O3' C O sing 1.43 N N
27 C1D C2D C C sing 1.55 N N
28 C1D O4D C O sing 1.44 N N
29 C1D O1D C O sing 1.43 N N
30 C2D O2D C O sing 1.43 N N
31 O5D PB O P sing 1.61 N N
32 O1B PB O P doub 1.48 N N
33 O2B PB O P sing 1.61 N N
34 O3A PB O P sing 1.61 N N
35 O3A PA O P sing 1.61 N N
36 O1A PA O P doub 1.48 N N
37 O2A PA O P sing 1.61 N N
38 O5' PA O P sing 1.61 N N
39 C4' H'4 C H sing 1.09 N N
40 C1' H'1 C H sing 1.09 N N
41 C2 H2 C H sing 1.08 N N
42 C3D HR'3 C H sing 1.09 N N
43 C4D HR'4 C H sing 1.09 N N
44 C5D H5R1 C H sing 1.09 N N
45 C5D H5R2 C H sing 1.09 N N
46 C5' H5'1 C H sing 1.09 N N
47 C5' H5'2 C H sing 1.09 N N
48 C2' H'2 C H sing 1.09 N N
49 C3' H'3 C H sing 1.09 N N
50 C2D HR'2 C H sing 1.09 N N
51 N6 H61 N H sing 0.97 N N
52 N6 H62 N H sing 0.97 N N
53 O3D HOR3 O H sing 0.97 N N
54 O2B HOB2 O H sing 0.97 N N
55 O2A HOA2 O H sing 0.97 N N
56 O2' HO'2 O H sing 0.97 N N
57 O3' HO'3 O H sing 0.97 N N
58 O1D HOR1 O H sing 0.97 N N
59 O2D HOR2 O H sing 0.97 N N
60 C4' O4' C O sing 1.44 N N
61 C4D O4D C O sing 1.44 N N
62 C1D HR'1 C H sing 1.09 N N



OI6 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
OI6 8azm Open in New Window Bound ligand 2 1