Chemical Components in the PDB

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B9X : Summary

Code

B9X

One-letter code

X

Molecule name

[(2R,3S,5R)-5-(6-aminopurin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] 3-(2-ethoxyethoxy)propanoate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 [(2~{R},3~{S},5~{R})-5-(6-aminopurin-9-yl)-2-(phosphonooxymethyl)oxolan-3-yl] 3-(2-ethoxyethoxy)propanoate

Formula

C17 H26 N5 O9 P

Formal charge

0

Molecular weight

475.39 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCOCCOCCC(=O)O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 2.0.6 CCOCCOCCC(=O)OC1CC(OC1COP(=O)(O)O)n2cnc3c2ncnc3N
Canonical SMILES CACTVS 3.385 CCOCCOCCC(=O)O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)n2cnc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 2.0.6 CCOCCOCCC(=O)O[C@H]1C[C@@H](O[C@@H]1COP(=O)(O)O)n2cnc3c2ncnc3N

IUPAC InChI

InChI=1S/C17H26N5O9P/c1-2-27-5-6-28-4-3-14(23)31-11-7-13(30-12(11)8-29-32(24,25)26)22-10-21-15-16(18)19-9-20-17(15)22/h9-13H,2-8H2,1H3,(H2,18,19,20)(H2,24,25,26)/t11-,12+,13+/m0/s1

IUPAC InChI key

YOZZSXDAZQISJN-YNEHKIRRSA-N
B9X

wwPDB Information

Atom count

58 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-03-14

Last modified at

2019-08-23

Status

Released

Obsoleted

Not Assigned



B9X : Atoms of Molecule

Total Number of Atoms: 58
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O9 O O1 N N N 0 -2.099 0.814 1.707
2 C10 C C1 N N N 0 -2.182 0.7 0.507
3 O1 O O2 N N N 0 -1.069 0.644 -0.241
4 C5 C C2 S N N 0 0.201 0.726 0.459
5 O O O3 N N N 0 2.338 0.43 -0.59
6 C8 C C3 R N N 0 1.27 1.38 -0.437
7 C9 C C4 N N N 0 1.798 2.653 0.228
8 P P P1 N N N 0 3.448 4.691 -0.286
9 C7 C C5 R N N 0 1.762 -0.883 -0.424
10 C6 C C6 N N N 0 0.757 -0.692 0.741
11 N2 N N1 N Y N 0 2.793 -1.857 -0.059
12 C1 C C7 N Y N 0 2.737 -3.213 -0.26
13 N1 N N2 N Y N 0 1.847 -4.047 -0.788
14 C C C8 N Y N 0 2.088 -5.341 -0.839
15 C4 C C9 N Y N 0 3.989 -1.581 0.536
16 N3 N N3 N Y N 0 4.66 -2.682 0.715
17 C2 C C10 N Y N 0 3.942 -3.73 0.245
18 C3 C C11 N Y N 0 4.153 -5.117 0.168
19 N4 N N4 N N N 0 5.321 -5.683 0.648
20 N N N5 N Y N 0 3.205 -5.872 -0.377
21 C11 C C12 N N N 0 -3.536 0.615 -0.15
22 C12 C C13 N N N 0 -4.627 0.697 0.919
23 O7 O O5 N N N 0 -8.423 -0.698 -0.176
24 O6 O O4 N N N 0 -5.911 0.616 0.296
25 C13 C C14 N N N 0 -7.006 0.683 1.212
26 C14 C C15 N N N 0 -8.323 0.587 0.439
27 C15 C C16 N N N 0 -9.623 -0.892 -0.927
28 C16 C C17 N N N 0 -9.622 -2.295 -1.537
29 O10 O O6 N N N 0 2.701 3.314 -0.66
30 O11 O O7 N N N 0 4.483 5.076 -1.458
31 O12 O O8 N N N 0 2.359 5.865 -0.125
32 H1 H H1 N N N 0 0.087 1.285 1.388
33 H2 H H2 N N N 0 0.842 1.617 -1.411
34 H3 H H3 N N N 0 0.963 3.316 0.456
35 H4 H H4 N N N 0 2.318 2.393 1.149
36 H5 H H5 N N N 0 1.246 -1.194 -1.332
37 H6 H H6 N N N 0 1.266 -0.725 1.704
38 H7 H H7 N N N 0 -0.038 -1.437 0.696
39 H8 H H8 N N N 0 1.344 -5.991 -1.275
40 H9 H H9 N N N 0 4.328 -0.595 0.816
41 H10 H H10 N N N 0 6.005 -5.121 1.044
42 H11 H H11 N N N 0 5.455 -6.642 0.589
43 H12 H H12 N N N 0 -3.652 1.442 -0.851
44 H13 H H13 N N N 0 -3.621 -0.33 -0.685
45 H14 H H14 N N N 0 -4.511 -0.13 1.62
46 H15 H H15 N N N 0 -4.542 1.642 1.454
47 H16 H H16 N N N 0 -6.939 -0.144 1.919
48 H17 H H17 N N N 0 -6.97 1.628 1.753
49 H18 H H18 N N N 0 -9.158 0.727 1.126
50 H19 H H19 N N N 0 -8.351 1.361 -0.329
51 H20 H H20 N N N 0 -10.485 -0.783 -0.269
52 H21 H H21 N N N 0 -9.677 -0.15 -1.723
53 H22 H H22 N N N 0 -9.567 -3.038 -0.741
54 H23 H H23 N N N 0 -10.537 -2.443 -2.11
55 H24 H H24 N N N 0 -8.76 -2.404 -2.196
56 H25 H H25 N N N 0 4.969 5.896 -1.3
57 H26 H H26 N N N 0 1.838 6.031 -0.923
58 O2 O O9 N N N 0 4.184 4.523 0.986



B9X : Chemical Bonds

Total Number of Bonds: 60
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C12 O C sing 1.43 N N
2 O6 C13 O C sing 1.43 N N
3 C16 C15 C C sing 1.53 N N
4 C12 C11 C C sing 1.53 N N
5 C13 C14 C C sing 1.53 N N
6 C15 O7 C O sing 1.43 N N
7 O7 C14 O C sing 1.43 N N
8 C11 C10 C C sing 1.51 N N
9 C10 O9 C O doub 1.21 N N
10 C10 O1 C O sing 1.34 N N
11 O1 C5 O C sing 1.45 N N
12 C6 C5 C C sing 1.55 N N
13 C6 C7 C C sing 1.55 N N
14 C5 C8 C C sing 1.54 N N
15 C N C N doub 1.32 N Y
16 C N1 C N sing 1.32 N Y
17 N C3 N C sing 1.33 N Y
18 N1 C1 N C doub 1.33 N Y
19 C3 N4 C N sing 1.38 N N
20 C3 C2 C C doub 1.41 N Y
21 C1 C2 C C sing 1.41 N Y
22 C1 N2 C N sing 1.37 N Y
23 C2 N3 C N sing 1.35 N Y
24 C7 N2 C N sing 1.46 N N
25 C7 O C O sing 1.44 N N
26 N2 C4 N C sing 1.36 N Y
27 N3 C4 N C doub 1.3 N Y
28 C8 O C O sing 1.44 N N
29 C8 C9 C C sing 1.53 N N
30 C9 O10 C O sing 1.43 N N
31 O11 P O P sing 1.61 N N
32 O10 P O P sing 1.61 N N
33 P O12 P O sing 1.61 N N
34 C5 H1 C H sing 1.09 N N
35 C8 H2 C H sing 1.09 N N
36 C9 H3 C H sing 1.09 N N
37 C9 H4 C H sing 1.09 N N
38 C7 H5 C H sing 1.09 N N
39 C6 H6 C H sing 1.09 N N
40 C6 H7 C H sing 1.09 N N
41 C H8 C H sing 1.08 N N
42 C4 H9 C H sing 1.08 N N
43 N4 H10 N H sing 0.97 N N
44 N4 H11 N H sing 0.97 N N
45 C11 H12 C H sing 1.09 N N
46 C11 H13 C H sing 1.09 N N
47 C12 H14 C H sing 1.09 N N
48 C12 H15 C H sing 1.09 N N
49 C13 H16 C H sing 1.09 N N
50 C13 H17 C H sing 1.09 N N
51 C14 H18 C H sing 1.09 N N
52 C14 H19 C H sing 1.09 N N
53 C15 H20 C H sing 1.09 N N
54 C15 H21 C H sing 1.09 N N
55 C16 H22 C H sing 1.09 N N
56 C16 H23 C H sing 1.09 N N
57 C16 H24 C H sing 1.09 N N
58 O11 H25 O H sing 0.97 N N
59 O12 H26 O H sing 0.97 N N
60 P O2 P O doub 1.48 N N



B9X : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
B9X 6ish Open in New Window Bound ligand 1 1