Chemical Components in the PDB

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08T : Summary

Code

08T

One-letter code

X

Molecule name

[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.2 [[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-oxidanyl-phosphoryl]oxy-tris(fluoranyl)beryllium

Formula

C10 H14 Be F3 N5 O10 P2

Formal charge

0

Molecular weight

492.201 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.370 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[Be](F)(F)F)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.7.2 [Be](OP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)n2cnc3c2ncnc3N)O)O)(F)(F)F
Canonical SMILES CACTVS 3.370 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)O[Be](F)(F)F)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.7.2 [Be](OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O)(F)(F)F

IUPAC InChI

InChI=1S/C10H15N5O10P2.Be.3FH/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20;;;;/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20);;3*1H/q;+4;;;/p-4/t4-,6-,7-,10-;;;;/m1..../s1

IUPAC InChI key

WOGYHYSOODLXII-KWIZKVQNSA-J
08T

wwPDB Information

Atom count

45 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-10-18

Last modified at

2011-12-30

Status

Released

Obsoleted

Not Assigned



08T : Atoms of Molecule

Total Number of Atoms: 45
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 BE BE BE N N N 0 6.712 1.379 1.127
2 C1' C C1' R N N 0 -3.342 -0.783 0.606
3 C2 C C2 N Y N 0 -7.372 0.984 1.49
4 C2' C C2' R N N 0 -3.676 -2.109 -0.123
5 C3' C C3' S N N 0 -2.404 -2.952 0.139
6 C4 C C4 N Y N 0 -5.35 0.748 0.424
7 C4' C C4' R N N 0 -1.322 -1.908 0.477
8 C5 C C5 N Y N 0 -5.674 1.833 -0.407
9 C5' C C5' N N N 0 -0.157 -2.027 -0.508
10 C6 C C6 N Y N 0 -6.915 2.466 -0.219
11 C8 C C8 N Y N 0 -3.707 1.134 -0.994
12 F1 F F1 N N N 0 7.031 1.975 2.342
13 F2 F F2 N N N 0 7.466 0.222 0.966
14 F3 F F3 N N N 0 6.992 2.262 0.09
15 H1 H H1 N N N 0 -0.503 -1.78 -1.511
16 H10 H H10 N N N 0 -8.058 0.644 2.252
17 H11 H H11 N N N 0 4.629 2.186 -1.427
18 H12 H H12 N N N 0 -8.148 3.968 -0.869
19 H13 H H13 N N N 0 -6.691 3.865 -1.7
20 H14 H H14 N N N 0 -2.766 1.052 -1.518
21 H2 H H2 N N N 0 0.225 -3.048 -0.497
22 H3 H H3 N N N 0 -0.963 -2.06 1.495
23 H4 H H4 N N N 0 -2.127 -3.512 -0.755
24 H5 H H5 N N N 0 -3.279 -4.515 1.084
25 H6 H H6 N N N 0 -3.819 -1.942 -1.191
26 H7 H H7 N N N 0 -5.023 -3.607 0.09
27 H8 H H8 N N N 0 -3.539 -0.872 1.674
28 H9 H H9 N N N 0 1.54 0.467 -2.414
29 N1 N N1 N Y N 0 -7.721 2.008 0.733
30 N3 N N3 N Y N 0 -6.221 0.361 1.35
31 N6 N N6 N N N 0 -7.288 3.54 -1.008
32 N7 N N7 N Y N 0 -4.629 2.016 -1.249
33 N9 N N9 N Y N 0 -4.105 0.328 0.03
34 O1A O O1A N N N 0 1.962 -0.403 -2.413
35 O1B O O1B N N N 0 5.574 -0.913 -0.463
36 O2' O O2' N N N 0 -4.827 -2.732 0.452
37 O2A O O2A N N N 0 2.906 -2.312 -1.058
38 O2B O O2B N N N 0 5.091 1.339 -1.495
39 O3' O O3' N N N 0 -2.608 -3.837 1.242
40 O3A O O3A N N N 0 3.249 0.022 -0.16
41 O3B O O3B N N N 0 5.312 1.046 1.108
42 O4' O O4' N N N 0 -1.93 -0.61 0.361
43 O5' O O5' N N N 0 0.883 -1.125 -0.127
44 PA P PA N N N 0 2.264 -0.984 -0.942
45 PB P PB N N N 0 4.823 0.346 -0.257



08T : Chemical Bonds

Total Number of Bonds: 47
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' C5' C C sing 1.53 N N
6 C4' O4' C O sing 1.44 N N
7 C2' C1' C C sing 1.55 N N
8 C5' O5' C O sing 1.43 N N
9 O4' C1' O C sing 1.44 N N
10 C1' N9 C N sing 1.47 N N
11 N3 C2 N C doub 1.32 N Y
12 N3 C4 N C sing 1.33 N Y
13 O2A PA O P doub 1.48 N N
14 C2 N1 C N sing 1.32 N Y
15 O5' PA O P sing 1.61 N N
16 C4 N9 C N sing 1.37 N Y
17 C4 C5 C C doub 1.4 N Y
18 N9 C8 N C sing 1.36 N Y
19 PA O1A P O sing 1.61 N N
20 PA O3A P O sing 1.61 N N
21 N1 C6 N C doub 1.33 N Y
22 C5 C6 C C sing 1.41 N Y
23 C5 N7 C N sing 1.35 N Y
24 O3A PB O P sing 1.61 N N
25 C8 N7 C N doub 1.3 N Y
26 C6 N6 C N sing 1.38 N N
27 O1B PB O P doub 1.48 N N
28 PB O3B P O sing 1.61 N N
29 PB O2B P O sing 1.61 N N
30 F1 BE F BE sing 1.39 N N
31 BE F3 BE F sing 1.39 N N
32 O3B BE O BE sing 1.44 N N
33 BE F2 BE F sing 1.39 N N
34 C5' H1 C H sing 1.09 N N
35 C5' H2 C H sing 1.09 N N
36 C4' H3 C H sing 1.09 N N
37 C3' H4 C H sing 1.09 N N
38 O3' H5 O H sing 0.97 N N
39 C2' H6 C H sing 1.09 N N
40 O2' H7 O H sing 0.97 N N
41 C1' H8 C H sing 1.09 N N
42 O1A H9 O H sing 0.97 N N
43 C2 H10 C H sing 1.08 N N
44 O2B H11 O H sing 0.97 N N
45 N6 H12 N H sing 0.97 N N
46 N6 H13 N H sing 0.97 N N
47 C8 H14 C H sing 1.08 N N



08T : Used in PDB Entries

Total Number of PDB Entries: 8
Ligand Code PDB Entry ID Type Total Distinct
08T 3u5z Open in New Window Bound ligand 6 1
08T 3u60 Open in New Window Bound ligand 3 1
08T 3u61 Open in New Window Bound ligand 2 1
08T 4ly6 Open in New Window Bound ligand 20 1
08T 4lzz Open in New Window Bound ligand 22 1
08T 6mii Open in New Window Bound ligand 3 1
08T 6qel Open in New Window Bound ligand 5 1
08T 6qem Open in New Window Bound ligand 5 1