Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

DX : Summary

Code

DX

One-letter code

X

Molecule name

[(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)imidazo[1,2-a][1,3,5]triazin-8-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.5 [(2~{R},3~{S},5~{R})-5-[2,4-bis(oxidanylidene)imidazo[1,2-a][1,3,5]triazin-8-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H13 N4 O8 P

Formal charge

0

Molecular weight

348.206 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 O[CH]1C[CH](O[CH]1CO[P](O)(O)=O)N2C=CN3C(=O)NC(=O)N=C23
SMILES OpenEye OEToolkits 2.0.5 C1C(C(OC1N2C=CN3C2=NC(=O)NC3=O)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.385 O[C@H]1C[C@@H](O[C@@H]1CO[P](O)(O)=O)N2C=CN3C(=O)NC(=O)N=C23
Canonical SMILES OpenEye OEToolkits 2.0.5 C1[C@@H]([C@H](O[C@H]1N2C=CN3C2=NC(=O)NC3=O)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C10H13N4O8P/c15-5-3-7(22-6(5)4-21-23(18,19)20)13-1-2-14-9(13)11-8(16)12-10(14)17/h1-2,5-7,15H,3-4H2,(H,12,16,17)(H2,18,19,20)/t5-,6+,7+/m0/s1

IUPAC InChI key

MIJXVMWIKXUKNK-RRKCRQDMSA-N
DX

wwPDB Information

Atom count

36 (23 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA linking

Type code

ATOMN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-07-19

Last modified at

2018-03-02

Status

Released

Obsoleted

Not Assigned



DX : Atoms of Molecule

Total Number of Atoms: 36
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P1 N N N 0 4.861 -1.083 -0.285
2 OP1 O O1 N N N 0 4.848 -1.705 1.058
3 O5' O O2 N N N 0 3.488 -0.274 -0.515
4 C5' C C1 N N N 0 3.023 0.74 0.378
5 C4' C C2 R N N 0 1.695 1.301 -0.135
6 C3' C C3 S N N 0 1.216 2.459 0.768
7 O3' O O3 N N N 0 1.557 3.72 0.189
8 C2' C C4 N N N 0 -0.318 2.285 0.82
9 C1' C C5 R N N 0 -0.585 1.042 -0.058
10 O4' O O4 N N N 0 0.657 0.302 -0.04
11 N9 N N1 N N N 0 -1.667 0.237 0.513
12 C4 C C6 N N N 0 -2.879 0.007 -0.058
13 N5 N N2 N N N 0 -3.59 -0.792 0.791
14 C7 C C7 N N N 0 -2.795 -1.051 1.896
15 C8 C C8 N N N 0 -1.633 -0.429 1.726
16 N3 N N3 N N N 0 -3.417 0.405 -1.202
17 C2 C C9 N N N 0 -4.655 0.03 -1.533
18 O2 O O5 N N N 0 -5.138 0.402 -2.588
19 N1 N N4 N N N 0 -5.372 -0.759 -0.71
20 C6 C C10 N N N 0 -4.84 -1.173 0.458
21 O6 O O6 N N N 0 -5.482 -1.885 1.206
22 OP2 O O7 N N N 0 6.106 -0.069 -0.395
23 H2 H H2 N N N 0 2.878 0.312 1.37
24 H3 H H3 N N N 0 3.759 1.541 0.433
25 H4 H H4 N N N 0 1.801 1.642 -1.165
26 H5 H H5 N N N 0 1.647 2.369 1.765
27 H6 H H6 N N N 0 1.28 4.483 0.715
28 H7 H H7 N N N 0 -0.647 2.106 1.844
29 H8 H H8 N N N 0 -0.818 3.16 0.405
30 H9 H H9 N N N 0 -0.831 1.342 -1.076
31 H10 H H10 N N N 0 -3.072 -1.655 2.747
32 H11 H H11 N N N 0 -0.802 -0.444 2.416
33 H13 H H13 N N N 0 -6.271 -1.028 -0.956
34 H14 H H14 N N N 0 6.177 0.376 -1.25
35 OP3 O O8 N N Y 0 5.003 -2.23 -1.406
36 H1 H H1 N N N 0 5.809 -2.759 -1.328



DX : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 C2 O C doub 1.22 N N
2 N1 C2 N C sing 1.35 N N
3 N1 C6 N C sing 1.35 N N
4 O6 C6 O C doub 1.22 N N
5 C2 N3 C N sing 1.34 N N
6 C6 N5 C N sing 1.35 N N
7 N3 C4 N C doub 1.33 N N
8 N5 C4 N C sing 1.37 N N
9 N5 C7 N C sing 1.39 N N
10 C4 N9 C N sing 1.36 N N
11 C7 C8 C C doub 1.33 N N
12 N9 C8 N C sing 1.38 N N
13 N9 C1' N C sing 1.46 N N
14 C2' C1' C C sing 1.55 N N
15 C2' C3' C C sing 1.54 N N
16 C1' O4' C O sing 1.45 N N
17 O5' P O P sing 1.61 N N
18 O5' C5' O C sing 1.43 N N
19 P OP1 P O doub 1.48 N N
20 P OP2 P O sing 1.61 N N
21 C3' O3' C O sing 1.43 N N
22 C3' C4' C C sing 1.54 N N
23 O4' C4' O C sing 1.44 N N
24 C4' C5' C C sing 1.53 N N
25 C5' H2 C H sing 1.09 N N
26 C5' H3 C H sing 1.09 N N
27 C4' H4 C H sing 1.09 N N
28 C3' H5 C H sing 1.09 N N
29 O3' H6 O H sing 0.97 N N
30 C2' H7 C H sing 1.09 N N
31 C2' H8 C H sing 1.09 N N
32 C1' H9 C H sing 1.09 N N
33 C7 H10 C H sing 1.08 N N
34 C8 H11 C H sing 1.08 N N
35 N1 H13 N H sing 0.97 N N
36 OP2 H14 O H sing 0.97 N N
37 P OP3 P O sing 1.61 N N
38 OP3 H1 O H sing 0.97 N N



DX : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
DX 5vbs Open in New Window Polymer component 2 2