Chemical Components in the PDB

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6R9 : Summary

Code

6R9

One-letter code

X

Molecule name

[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.5 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] ethanoate

Formula

C12 H16 N5 O8 P

Formal charge

0

Molecular weight

389.258 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC(=O)O[P](O)(=O)OC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23
SMILES OpenEye OEToolkits 2.0.5 CC(=O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O
Canonical SMILES CACTVS 3.385 CC(=O)O[P](O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23
Canonical SMILES OpenEye OEToolkits 2.0.5 CC(=O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O

IUPAC InChI

InChI=1S/C12H16N5O8P/c1-5(18)25-26(21,22)23-2-6-8(19)9(20)12(24-6)17-4-16-7-10(13)14-3-15-11(7)17/h3-4,6,8-9,12,19-20H,2H2,1H3,(H,21,22)(H2,13,14,15)/t6-,8-,9-,12-/m1/s1

IUPAC InChI key

UBPVOHPZRZIJHM-WOUKDFQISA-N
6R9

wwPDB Information

Atom count

42 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-05-31

Last modified at

2016-07-08

Status

Released

Obsoleted

Not Assigned



6R9 : Atoms of Molecule

Total Number of Atoms: 42
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C1 N N N 0 -6.777 -2.276 1.77
2 C02 C C2 N N N 0 -6.087 -1.443 0.721
3 C09 C C3 N N N 0 -1.89 1.233 -0.562
4 C10 C C4 R N N 0 -0.571 1.493 0.168
5 C11 C C5 S N N 0 0.263 2.552 -0.588
6 C12 C C6 R N N 0 1.721 2.065 -0.429
7 C13 C C7 R N N 0 1.596 0.769 0.403
8 C16 C C8 N Y N 0 2.345 -1.223 -0.951
9 C18 C C9 N Y N 0 4.416 -1.422 -0.339
10 C19 C C10 N Y N 0 3.879 -0.322 0.352
11 C21 C C11 N Y N 0 5.913 0.01 1.369
12 C23 C C12 N Y N 0 5.762 -1.754 -0.112
13 N15 N N1 N Y N 0 2.571 -0.225 -0.051
14 N17 N N2 N Y N 0 3.429 -1.924 -1.119
15 N20 N N3 N Y N 0 4.656 0.358 1.188
16 N22 N N4 N Y N 0 6.462 -1.015 0.743
17 N24 N N5 N N N 0 6.346 -2.827 -0.763
18 O03 O O1 N N N 0 -6.673 -1.138 -0.291
19 O04 O O2 N N N 0 -4.821 -1.038 0.91
20 O06 O O3 N N N 0 -5.008 1.026 -0.53
21 O07 O O4 N N N 0 -4.019 -1.039 -1.594
22 O08 O O5 N N N 0 -2.695 0.341 0.211
23 O14 O O6 N N N 0 0.25 0.304 0.162
24 O25 O O7 N N N 0 2.5 3.037 0.271
25 O26 O O8 N N N 0 0.097 3.839 0.01
26 P05 P P1 N N N 0 -4.154 -0.152 -0.257
27 H1 H H1 N N N 0 -6.815 -1.721 2.707
28 H2 H H2 N N N 0 -7.79 -2.506 1.442
29 H3 H H3 N N N 0 -6.223 -3.203 1.919
30 H4 H H4 N N N 0 -2.421 2.175 -0.7
31 H5 H H5 N N N 0 -1.684 0.787 -1.536
32 H6 H H6 N N N 0 -0.762 1.819 1.19
33 H7 H H7 N N N 0 -0.02 2.581 -1.64
34 H8 H H8 N N N 0 2.161 1.854 -1.403
35 H9 H H9 N N N 0 1.738 0.984 1.463
36 H10 H H10 N N N 0 1.404 -1.408 -1.449
37 H11 H H11 N N N 0 6.518 0.584 2.055
38 H12 H H12 N N N 0 5.825 -3.359 -1.384
39 H13 H H13 N N N 0 7.276 -3.046 -0.598
40 H14 H H14 N N N 0 -3.472 -1.829 -1.488
41 H15 H H15 N N N 0 2.561 3.89 -0.179
42 H16 H H16 N N N 0 0.599 4.542 -0.425



6R9 : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C01 C02 C C sing 1.51 N N
2 O03 C02 O C doub 1.21 N N
3 O06 P05 O P doub 1.48 N N
4 C02 O04 C O sing 1.34 N N
5 O04 P05 O P sing 1.61 N N
6 N24 C23 N C sing 1.38 N N
7 P05 O08 P O sing 1.61 N N
8 P05 O07 P O sing 1.61 N N
9 N17 C16 N C doub 1.3 N Y
10 N17 C18 N C sing 1.35 N Y
11 C16 N15 C N sing 1.36 N Y
12 O08 C09 O C sing 1.43 N N
13 C23 C18 C C doub 1.4 N Y
14 C23 N22 C N sing 1.33 N Y
15 C18 C19 C C sing 1.41 N Y
16 O14 C13 O C sing 1.44 N N
17 O14 C10 O C sing 1.44 N N
18 N15 C19 N C sing 1.37 N Y
19 N15 C13 N C sing 1.46 N N
20 N22 C21 N C doub 1.32 N Y
21 C19 N20 C N doub 1.33 N Y
22 C09 C10 C C sing 1.53 N N
23 C13 C12 C C sing 1.55 N N
24 C21 N20 C N sing 1.32 N Y
25 C10 C11 C C sing 1.55 N N
26 C12 C11 C C sing 1.55 N N
27 C12 O25 C O sing 1.43 N N
28 C11 O26 C O sing 1.43 N N
29 C01 H1 C H sing 1.09 N N
30 C01 H2 C H sing 1.09 N N
31 C01 H3 C H sing 1.09 N N
32 C09 H4 C H sing 1.09 N N
33 C09 H5 C H sing 1.09 N N
34 C10 H6 C H sing 1.09 N N
35 C11 H7 C H sing 1.09 N N
36 C12 H8 C H sing 1.09 N N
37 C13 H9 C H sing 1.09 N N
38 C16 H10 C H sing 1.08 N N
39 C21 H11 C H sing 1.08 N N
40 N24 H12 N H sing 0.97 N N
41 N24 H13 N H sing 0.97 N N
42 O07 H14 O H sing 0.97 N N
43 O25 H15 O H sing 0.97 N N
44 O26 H16 O H sing 0.97 N N



6R9 : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
6R9 5k8f Open in New Window Bound ligand 3 1
6R9 7l4g Open in New Window Bound ligand 3 1
6R9 8biq Open in New Window Bound ligand 1 1
6R9 8bit Open in New Window Bound ligand 2 1