Chemical Components in the PDB

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0FT : Summary

Code

0FT

One-letter code

X

Molecule name

1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine

Systematic names

ProgramVersionName
ACDLabs 12.01 1-{[1-(alpha-L-arabinofuranosyl)-1H-1,2,3-triazol-4-yl]methyl}-5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidine
OpenEye OEToolkits 1.7.6 1-[[1-[(2R,3R,4R,5S)-5-(hydroxymethyl)-3,4-bis(oxidanyl)oxolan-2-yl]-1,2,3-triazol-4-yl]methyl]-5-methyl-pyrimidine-2,4-dione

Formula

C13 H17 N5 O6

Formal charge

0

Molecular weight

339.304 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1C(=CN(C(=O)N1)Cc2nnn(c2)C3OC(C(O)C3O)CO)C
SMILES CACTVS 3.370 CC1=CN(Cc2cn(nn2)[CH]3O[CH](CO)[CH](O)[CH]3O)C(=O)NC1=O
SMILES OpenEye OEToolkits 1.7.6 CC1=CN(C(=O)NC1=O)Cc2cn(nn2)C3C(C(C(O3)CO)O)O
Canonical SMILES CACTVS 3.370 CC1=CN(Cc2cn(nn2)[C@@H]3O[C@@H](CO)[C@H](O)[C@H]3O)C(=O)NC1=O
Canonical SMILES OpenEye OEToolkits 1.7.6 CC1=CN(C(=O)NC1=O)Cc2cn(nn2)[C@H]3[C@@H]([C@H]([C@@H](O3)CO)O)O

IUPAC InChI

InChI=1S/C13H17N5O6/c1-6-2-17(13(23)14-11(6)22)3-7-4-18(16-15-7)12-10(21)9(20)8(5-19)24-12/h2,4,8-10,12,19-21H,3,5H2,1H3,(H,14,22,23)/t8-,9-,10+,12+/m0/s1

IUPAC InChI key

FVDUYFCPFLONHE-UXCLJVHYSA-N
0FT

wwPDB Information

Atom count

41 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-08-10

Last modified at

2012-11-16

Status

Released

Obsoleted

Not Assigned



0FT : Atoms of Molecule

Total Number of Atoms: 41
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 2.498 0.269 -0.475
2 C2 C C2 N N N 0 -3.36 0.045 -1.309
3 C2' C C2' R N N 0 3.651 1.145 0.075
4 C3' C C3' R N N 0 4.824 0.126 0.071
5 C4 C C4 N N N 0 -4.888 -1.196 -0.051
6 C4' C C4' S N N 0 4.107 -1.199 0.407
7 C5 C C5 N N N 0 -4.676 -0.325 1.045
8 C5' C C5' N N N 0 4.705 -2.339 -0.42
9 C5A C C5A N N N 0 -5.41 -0.538 2.344
10 C6 C C6 N N N 0 -3.807 0.7 0.911
11 C7 C C7 N N N 0 -2.206 1.992 -0.421
12 C8 C C8 N Y N 0 -0.828 1.538 -0.013
13 C9 C C9 N Y N 0 0.15 1.082 -0.83
14 H1 H H1 N N N 0 -3.632 1.375 1.735
15 H10 H H10 N N N 0 4.213 -1.418 1.469
16 H11 H H11 N N N 0 4.508 -2.163 -1.478
17 H12 H H12 N N N 0 5.781 -2.383 -0.253
18 H13 H H13 N N N 0 4.443 -4.345 -0.509
19 H14 H H14 N N N 0 5.293 0.075 -0.912
20 H15 H H15 N N N 0 6.263 1.278 0.91
21 H16 H H16 N N N 0 3.435 1.49 1.086
22 H17 H H17 N N N 0 4.637 2.821 -0.491
23 H2 H H2 N N N 0 -2.52 2.82 0.214
24 H3 H H3 N N N 0 -2.188 2.319 -1.461
25 H4 H H4 N N N 0 0.098 0.969 -1.902
26 H5 H H5 N N N 0 -4.36 -1.577 -1.958
27 H6 H H6 N N N 0 -6.35 0.014 2.325
28 H7 H H7 N N N 0 -5.615 -1.6 2.475
29 H8 H H8 N N N 0 -4.796 -0.182 3.171
30 H9 H H9 N N N 0 2.537 0.229 -1.563
31 N1 N N1 N N N 0 -3.149 0.88 -0.275
32 N3 N N3 N N N 0 -4.22 -0.985 -1.203
33 N5 N N5 N Y N 0 -0.329 1.513 1.228
34 N6 N N6 N Y N 0 0.877 1.066 1.183
35 N7 N N7 N Y N 0 1.204 0.795 -0.032
36 O2 O O2 N N N 0 -2.765 0.223 -2.355
37 O2' O O2' N N N 0 3.922 2.246 -0.795
38 O3' O O3' N N N 0 5.786 0.453 1.075
39 O4 O O4 N N N 0 -5.663 -2.13 0.048
40 O4' O O4' N N N 0 2.721 -1.037 0.08
41 O5' O O5' N N N 0 4.11 -3.577 -0.025



0FT : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2' C2' O C sing 1.43 N N
2 C2' C1' C C sing 1.55 N N
3 C2' C3' C C sing 1.55 N N
4 O5' C5' O C sing 1.43 N N
5 C1' O4' C O sing 1.44 N N
6 C1' N7 C N sing 1.47 N N
7 C5' C4' C C sing 1.53 N N
8 C5A C5 C C sing 1.51 N N
9 O4' C4' O C sing 1.43 N N
10 C3' C4' C C sing 1.54 N N
11 C3' O3' C O sing 1.43 N N
12 C9 N7 C N sing 1.35 N Y
13 C9 C8 C C doub 1.35 N Y
14 N7 N6 N N sing 1.29 N Y
15 C5 C6 C C doub 1.35 N N
16 C5 C4 C C sing 1.42 N N
17 C6 N1 C N sing 1.37 N N
18 O4 C4 O C doub 1.22 N N
19 C4 N3 C N sing 1.35 N N
20 C8 C7 C C sing 1.51 N N
21 C8 N5 C N sing 1.34 N Y
22 N6 N5 N N doub 1.29 N Y
23 N1 C7 N C sing 1.47 N N
24 N1 C2 N C sing 1.35 N N
25 N3 C2 N C sing 1.35 N N
26 C2 O2 C O doub 1.22 N N
27 C6 H1 C H sing 1.08 N N
28 C7 H2 C H sing 1.09 N N
29 C7 H3 C H sing 1.09 N N
30 C9 H4 C H sing 1.08 N N
31 N3 H5 N H sing 0.97 N N
32 C5A H6 C H sing 1.09 N N
33 C5A H7 C H sing 1.09 N N
34 C5A H8 C H sing 1.09 N N
35 C1' H9 C H sing 1.09 N N
36 C4' H10 C H sing 1.09 N N
37 C5' H11 C H sing 1.09 N N
38 C5' H12 C H sing 1.09 N N
39 O5' H13 O H sing 0.97 N N
40 C3' H14 C H sing 1.09 N N
41 O3' H15 O H sing 0.97 N N
42 C2' H16 C H sing 1.09 N N
43 O2' H17 O H sing 0.97 N N



0FT : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0FT 4g8y Open in New Window Bound ligand 1 1