Chemical Components in the PDB

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QSQ : Summary

Code

QSQ

One-letter code

A

Molecule name

[(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-(trifluoromethyloxy)oxolan-2-yl]methyl dihydrogen phosphite

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [(2~{R},3~{R},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3-oxidanyl-4-(trifluoromethyloxy)oxolan-2-yl]methyl dihydrogen phosphite

Formula

C11 H13 F3 N5 O6 P

Formal charge

0

Molecular weight

399.22 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](COP(O)O)[CH](O)[CH]3OC(F)(F)F
SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(O)O)O)OC(F)(F)F)N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](COP(O)O)[C@@H](O)[C@H]3OC(F)(F)F
Canonical SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(O)O)O)OC(F)(F)F)N

IUPAC InChI

InChI=1S/C11H13F3N5O6P/c12-11(13,14)25-7-6(20)4(1-23-26(21)22)24-10(7)19-3-18-5-8(15)16-2-17-9(5)19/h2-4,6-7,10,20-22H,1H2,(H2,15,16,17)/t4-,6-,7-,10-/m1/s1

IUPAC InChI key

QTJSXSSMPAZFOY-KQYNXXCUSA-N
QSQ

wwPDB Information

Atom count

39 (26 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

A

Defined at

2020-07-31

Last modified at

2020-12-11

Status

Released

Obsoleted

Not Assigned



QSQ : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1 R N N 0 -0.14 -0.097 -0.55
2 C2 C C2 N Y N 0 -4.399 -1.118 -1.533
3 C2' C C3 R N N 0 -0.281 1.24 0.211
4 C23 C C4 N N N 0 -1.753 3.131 0.275
5 C3' C C5 R N N 0 1.168 1.763 0.322
6 C4 C C6 N Y N 0 -2.38 -1.271 -0.445
7 C4' C C7 R N N 0 2.014 0.68 -0.385
8 C5 C C8 N Y N 0 -2.894 -2.318 0.338
9 C5' C C9 N N N 0 3.347 0.488 0.34
10 C6 C C10 N Y N 0 -4.221 -2.723 0.116
11 C8 C C11 N Y N 0 -0.845 -1.987 0.966
12 F24 F F1 N N N 0 -2.593 2.486 1.188
13 F25 F F2 N N N 0 -2.512 3.973 -0.544
14 F26 F F3 N N N 0 -0.802 3.887 0.969
15 N1 N N1 N Y N 0 -4.925 -2.098 -0.822
16 N3 N N2 N Y N 0 -3.161 -0.705 -1.36
17 N6 N N3 N N N 0 -4.782 -3.749 0.856
18 N7 N N4 N Y N 0 -1.906 -2.71 1.178
19 N9 N N5 N Y N 0 -1.087 -1.085 -0.026
20 O2' O O1 N N N 0 -1.088 2.156 -0.532
21 O3' O O2 N N N 0 1.301 3.018 -0.348
22 O4' O O3 N N N 0 1.218 -0.522 -0.302
23 O5' O O4 N N N 0 4.16 -0.43 -0.393
24 OP1 O O5 N N N 0 5.325 -2.152 1.0
25 OP2 O O6 N N N 0 6.229 -1.545 -1.253
26 P P P1 N N N 0 5.636 -0.867 0.081
27 H1 H H1 N N N 0 -0.301 0.053 -1.618
28 H2 H H2 N N N 0 -5.005 -0.64 -2.288
29 H3 H H3 N N N 0 -0.704 1.072 1.201
30 H4 H H4 N N N 0 1.462 1.855 1.368
31 H5 H H5 N N N 0 2.185 0.953 -1.426
32 H6 H H6 N N N 0 3.861 1.446 0.418
33 H7 H H7 N N N 0 3.164 0.093 1.339
34 H8 H H8 N N N 0 0.09 -2.088 1.498
35 H9 H H9 N N N 0 -4.257 -4.198 1.538
36 H10 H H10 N N N 0 -5.699 -4.02 0.694
37 H11 H H11 N N N 0 2.191 3.393 -0.31
38 H12 H H12 N N N 0 6.113 -2.561 1.383
39 H13 H H13 N N N 0 7.132 -1.877 -1.158



QSQ : Chemical Bonds

Total Number of Bonds: 41
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 F25 C23 F C sing 1.4 N N
3 O2' C23 O C sing 1.43 N N
4 O2' C2' O C sing 1.43 N N
5 C23 F26 C F sing 1.4 N N
6 C23 F24 C F sing 1.4 N N
7 C2' C3' C C sing 1.54 N N
8 C2' C1' C C sing 1.54 N N
9 C3' C4' C C sing 1.55 N N
10 C2 N3 C N doub 1.32 N Y
11 C2 N1 C N sing 1.32 N Y
12 N3 C4 N C sing 1.33 N Y
13 C4' C5' C C sing 1.53 N N
14 C4' O4' C O sing 1.44 N N
15 C1' N9 C N sing 1.47 N N
16 C1' O4' C O sing 1.44 N N
17 N1 C6 N C doub 1.33 N Y
18 C4 N9 C N sing 1.37 N Y
19 C4 C5 C C doub 1.4 N Y
20 N9 C8 N C sing 1.36 N Y
21 C5' O5' C O sing 1.43 N N
22 C6 C5 C C sing 1.41 N Y
23 C6 N6 C N sing 1.38 N N
24 O5' P O P sing 1.61 N N
25 C5 N7 C N sing 1.35 N Y
26 OP1 P O P sing 1.61 N N
27 C8 N7 C N doub 1.3 N Y
28 P OP2 P O sing 1.61 N N
29 C1' H1 C H sing 1.09 N N
30 C2 H2 C H sing 1.08 N N
31 C2' H3 C H sing 1.09 N N
32 C3' H4 C H sing 1.09 N N
33 C4' H5 C H sing 1.09 N N
34 C5' H6 C H sing 1.09 N N
35 C5' H7 C H sing 1.09 N N
36 C8 H8 C H sing 1.08 N N
37 N6 H9 N H sing 0.97 N N
38 N6 H10 N H sing 0.97 N N
39 O3' H11 O H sing 0.97 N N
40 OP1 H12 O H sing 0.97 N N
41 OP2 H13 O H sing 0.97 N N



QSQ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
QSQ 6zxz Open in New Window Polymer component 3 1