Chemical Components in the PDB

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8ZB : Summary

Code

8ZB

One-letter code

X

Molecule name

(2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (2~{R},3~{R},4~{S},5~{R})-2-(6-aminopurin-9-yl)-5-propyl-oxolane-3,4-diol

Formula

C12 H17 N5 O3

Formal charge

0

Molecular weight

279.295 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 2.0.6 CCCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Canonical SMILES CACTVS 3.385 CCC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 2.0.6 CCC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O

IUPAC InChI

InChI=1S/C12H17N5O3/c1-2-3-6-8(18)9(19)12(20-6)17-5-16-7-10(13)14-4-15-11(7)17/h4-6,8-9,12,18-19H,2-3H2,1H3,(H2,13,14,15)/t6-,8-,9-,12-/m1/s1

IUPAC InChI key

BKDAOQOLDUJANJ-WOUKDFQISA-N
8ZB

wwPDB Information

Atom count

37 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-03-30

Last modified at

2017-03-31

Status

Released

Obsoleted

Not Assigned



8ZB : Atoms of Molecule

Total Number of Atoms: 37
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C24 C C1 N N N 0 5.646 -2.452 -0.329
2 C28 C C2 N N N 0 4.477 -1.609 -0.843
3 C31 C C3 N N N 0 4.042 -0.624 0.244
4 C36 C C4 R N N 0 2.873 0.219 -0.27
5 C38 C C5 R N N 0 0.584 0.34 -0.395
6 C39 C C6 R N N 0 0.957 1.386 0.679
7 C40 C C7 S N N 0 2.498 1.305 0.763
8 C49 C C8 N Y N 0 -0.766 -1.53 0.63
9 C50 C C9 N Y N 0 -2.796 -0.881 0.231
10 C51 C C10 N Y N 0 -1.934 0.097 -0.293
11 C53 C C11 N Y N 0 -3.759 1.309 -0.989
12 C55 C C12 N Y N 0 -4.181 -0.682 0.1
13 N47 N N1 N Y N 0 -0.66 -0.342 -0.031
14 N48 N N2 N Y N 0 -2.02 -1.844 0.783
15 N52 N N3 N Y N 0 -2.454 1.165 -0.889
16 N54 N N4 N Y N 0 -4.608 0.417 -0.512
17 N57 N N5 N N N 0 -5.079 -1.611 0.596
18 O37 O O1 N N N 0 1.686 -0.593 -0.4
19 O41 O O2 N N N 0 0.547 2.692 0.27
20 O42 O O3 N N N 0 3.086 2.558 0.408
21 H2 H H1 N N N 0 6.481 -1.799 -0.075
22 H1 H H2 N N N 0 5.334 -3.004 0.557
23 H29 H H3 N N N 0 5.956 -3.153 -1.104
24 H28 H H4 N N N 0 4.79 -1.057 -1.73
25 H33 H H5 N N N 0 3.642 -2.262 -1.097
26 H35 H H6 N N N 0 3.73 -1.176 1.13
27 H31 H H7 N N N 0 4.877 0.029 0.498
28 H61 H H8 N N N 0 3.128 0.677 -1.226
29 H62 H H9 N N N 0 0.486 0.816 -1.37
30 H44 H H10 N N N 0 0.507 1.128 1.637
31 H43 H H11 N N N 0 2.811 1.005 1.763
32 H58 H H12 N N N 0 0.068 -2.124 0.973
33 H56 H H13 N N N 0 -4.149 2.188 -1.479
34 H60 H H14 N N N 0 -4.755 -2.41 1.04
35 H59 H H15 N N N 0 -6.033 -1.463 0.499
36 H46 H H16 N N N 0 0.757 3.388 0.908
37 H45 H H17 N N N 0 2.883 3.276 1.023



8ZB : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N57 C55 N C sing 1.38 N N
2 C55 C50 C C doub 1.41 N Y
3 C55 N54 C N sing 1.33 N Y
4 N48 C50 N C sing 1.35 N Y
5 N48 C49 N C doub 1.3 N Y
6 C50 C51 C C sing 1.41 N Y
7 N54 C53 N C doub 1.32 N Y
8 C49 N47 C N sing 1.36 N Y
9 C51 N47 C N sing 1.37 N Y
10 C51 N52 C N doub 1.33 N Y
11 C53 N52 C N sing 1.32 N Y
12 N47 C38 N C sing 1.46 N N
13 C38 C39 C C sing 1.54 N N
14 C38 O37 C O sing 1.44 N N
15 C39 O41 C O sing 1.43 N N
16 C39 C40 C C sing 1.55 N N
17 O37 C36 O C sing 1.44 N N
18 C31 C36 C C sing 1.53 N N
19 C31 C28 C C sing 1.53 N N
20 C24 C28 C C sing 1.53 N N
21 C36 C40 C C sing 1.55 N N
22 C40 O42 C O sing 1.43 N N
23 C24 H2 C H sing 1.09 N N
24 C24 H1 C H sing 1.09 N N
25 C24 H29 C H sing 1.09 N N
26 C28 H28 C H sing 1.09 N N
27 C28 H33 C H sing 1.09 N N
28 C31 H35 C H sing 1.09 N N
29 C31 H31 C H sing 1.09 N N
30 C36 H61 C H sing 1.09 N N
31 C38 H62 C H sing 1.09 N N
32 C39 H44 C H sing 1.09 N N
33 C40 H43 C H sing 1.09 N N
34 C49 H58 C H sing 1.08 N N
35 C53 H56 C H sing 1.08 N N
36 N57 H60 N H sing 0.97 N N
37 N57 H59 N H sing 0.97 N N
38 O41 H46 O H sing 0.97 N N
39 O42 H45 O H sing 0.97 N N



8ZB : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
8ZB 5lgp Open in New Window Bound ligand 4 1
8ZB 5lgq Open in New Window Bound ligand 4 1
8ZB 6h9f Open in New Window Bound ligand 2 1