Chemical Components in the PDB

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GP0 : Summary

Code

GP0

One-letter code

X

Molecule name

5-fluoro-1-[3-C-(hydroxymethyl)-beta-D-glucopyranosyl]pyrimidine-2,4(1H,3H)-dione

Systematic names

ProgramVersionName
ACDLabs 12.01 5-fluoro-1-[3-C-(hydroxymethyl)-beta-D-glucopyranosyl]pyrimidine-2,4(1H,3H)-dione
OpenEye OEToolkits 1.7.2 1-[(2R,3R,4S,5R,6R)-4,6-bis(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]-5-fluoranyl-pyrimidine-2,4-dione

Formula

C11 H15 F N2 O8

Formal charge

0

Molecular weight

322.244 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 FC1=CN(C(=O)NC1=O)C2OC(C(O)C(O)(C2O)CO)CO
SMILES CACTVS 3.370 OC[CH]1O[CH]([CH](O)[C](O)(CO)[CH]1O)N2C=C(F)C(=O)NC2=O
SMILES OpenEye OEToolkits 1.7.2 C1=C(C(=O)NC(=O)N1C2C(C(C(C(O2)CO)O)(CO)O)O)F
Canonical SMILES CACTVS 3.370 OC[C@H]1O[C@H]([C@H](O)[C@](O)(CO)[C@@H]1O)N2C=C(F)C(=O)NC2=O
Canonical SMILES OpenEye OEToolkits 1.7.2 C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@]([C@@H]([C@H](O2)CO)O)(CO)O)O)F

IUPAC InChI

InChI=1S/C11H15FN2O8/c12-4-1-14(10(20)13-8(4)19)9-7(18)11(21,3-16)6(17)5(2-15)22-9/h1,5-7,9,15-18,21H,2-3H2,(H,13,19,20)/t5-,6-,7+,9-,11+/m1/s1

IUPAC InChI key

ASRLDHHNHXDEKP-RZBPYSQRSA-N
GP0

wwPDB Information

Atom count

37 (22 without Hydrogen)

Polymer type

Saccharide

Type description

D-saccharide

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2011-08-10

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



GP0 : Atoms of Molecule

Total Number of Atoms: 37
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1A C C1 N N N 0 2.275 -0.367 -1.119
2 F1 F F1 N N N 0 4.478 -0.658 -1.868
3 N1 N N1 N N N 0 1.405 0.01 -0.129
4 C2A C C2 N N N 0 3.606 -0.291 -0.904
5 C3A C C3 N N N 0 4.076 0.181 0.348
6 O3A O O3 N N N 0 5.271 0.259 0.566
7 N4 N N4 N N N 0 3.186 0.541 1.295
8 C5A C C5 N N N 0 1.865 0.456 1.054
9 O5A O O5 N N N 0 1.076 0.785 1.918
10 C1 C C1' R N N 0 -0.039 -0.073 -0.361
11 C2 C C2' R N N 0 -0.649 -1.113 0.582
12 O2 O O2' N N N 0 -0.096 -2.399 0.297
13 C3 C C3' S N N 0 -2.167 -1.151 0.376
14 O3 O O3' N N N 0 -2.753 -2.066 1.304
15 C4 C C4' R N N 0 -2.737 0.252 0.608
16 O4 O O4' N N N 0 -4.142 0.245 0.347
17 C5 C C5' R N N 0 -2.047 1.239 -0.336
18 O5 O O5' N N N 0 -0.636 1.202 -0.113
19 C6 C C6' N N N 0 -2.569 2.652 -0.068
20 O6 O O6' N N N 0 -2.012 3.555 -1.026
21 C7' C C7' N N N 0 -2.477 -1.601 -1.053
22 H1A H H1 N N N 0 1.898 -0.728 -2.064
23 HN4 H HN4 N N N 0 3.5 0.865 2.154
24 H1 H H1' N N N 0 -0.225 -0.367 -1.394
25 H2 H H2' N N N 0 -0.428 -0.842 1.615
26 HO2 H HO2' N N Y 0 0.864 -2.447 0.403
27 HO3 H HO3' N N Y 0 -3.714 -2.14 1.229
28 H4 H H4' N N N 0 -2.56 0.55 1.642
29 HO4 H HO4' N N Y 0 -4.571 1.102 0.475
30 H5 H H5' N N N 0 -2.259 0.962 -1.369
31 H61 H H6' N N N 0 -3.655 2.659 -0.151
32 H62 H H6'A N N N 0 -2.278 2.962 0.935
33 HO6 H HO6' N N Y 0 -2.3 4.471 -0.916
34 H7' H H7' N N N 0 -2.143 -2.629 -1.191
35 O7' O O7' N N N 0 -3.886 -1.524 -1.281
36 H14 H H14 N N N 0 -1.959 -0.952 -1.759
37 H15 H H15 N N N 0 -4.156 -1.796 -2.169



GP0 : 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 C1A N1 C N sing 1.37 N N
2 C1A C2A C C doub 1.35 N N
3 C1A H1A C H sing 1.08 N N
4 F1 C2A F C sing 1.35 N N
5 N1 C5A N C sing 1.35 N N
6 N1 C1 N C sing 1.46 N N
7 C2A C3A C C sing 1.42 N N
8 C3A O3A C O doub 1.22 N N
9 C3A N4 C N sing 1.35 N N
10 N4 C5A N C sing 1.35 N N
11 N4 HN4 N H sing 0.97 N N
12 C5A O5A C O doub 1.22 N N
13 C1 C2 C C sing 1.53 N N
14 C1 O5 C O sing 1.43 N N
15 C1 H1 C H sing 1.09 N N
16 C2 O2 C O sing 1.43 N N
17 C2 C3 C C sing 1.53 N N
18 C2 H2 C H sing 1.09 N N
19 O2 HO2 O H sing 0.97 N N
20 C3 O3 C O sing 1.43 N N
21 C3 C4 C C sing 1.53 N N
22 C3 C7' C C sing 1.53 N N
23 O3 HO3 O H sing 0.97 N N
24 C4 O4 C O sing 1.43 N N
25 C4 C5 C C sing 1.53 N N
26 C4 H4 C H sing 1.09 N N
27 O4 HO4 O H sing 0.97 N N
28 C5 O5 C O sing 1.43 N N
29 C5 C6 C C sing 1.53 N N
30 C5 H5 C H sing 1.09 N N
31 C6 O6 C O sing 1.43 N N
32 C6 H61 C H sing 1.09 N N
33 C6 H62 C H sing 1.09 N N
34 O6 HO6 O H sing 0.97 N N
35 C7' H7' C H sing 1.09 N N
36 C7' O7' C O sing 1.43 N N
37 C7' H14 C H sing 1.09 N N
38 O7' H15 O H sing 0.97 N N



GP0 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
GP0 3sym Open in New Window Bound ligand 1 1