Chemical Components in the PDB

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F2U : Summary

Code

F2U

One-letter code

X

Molecule name

2'-deoxy-5-ethynyl-2',2'-difluorouridine

Systematic names

ProgramVersionName
ACDLabs 12.01 2'-deoxy-5-ethynyl-2',2'-difluorouridine
OpenEye OEToolkits 1.7.6 1-[(2R,4R,5R)-3,3-bis(fluoranyl)-5-(hydroxymethyl)-4-oxidanyl-oxolan-2-yl]-5-ethynyl-pyrimidine-2,4-dione

Formula

C11 H10 F2 N2 O5

Formal charge

0

Molecular weight

288.204 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1NC(=O)N(C=C1C#C)C2OC(C(O)C2(F)F)CO
SMILES CACTVS 3.370 OC[CH]1O[CH](N2C=C(C#C)C(=O)NC2=O)C(F)(F)[CH]1O
SMILES OpenEye OEToolkits 1.7.6 C#CC1=CN(C(=O)NC1=O)C2C(C(C(O2)CO)O)(F)F
Canonical SMILES CACTVS 3.370 OC[C@H]1O[C@@H](N2C=C(C#C)C(=O)NC2=O)C(F)(F)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 1.7.6 C#CC1=CN(C(=O)NC1=O)[C@H]2C([C@@H]([C@H](O2)CO)O)(F)F

IUPAC InChI

InChI=1S/C11H10F2N2O5/c1-2-5-3-15(10(19)14-8(5)18)9-11(12,13)7(17)6(4-16)20-9/h1,3,6-7,9,16-17H,4H2,(H,14,18,19)/t6-,7-,9-/m1/s1

IUPAC InChI key

JFVJRPYRLUHQTG-ZXFLCMHBSA-N
F2U

wwPDB Information

Atom count

30 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-02-12

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



F2U : Atoms of Molecule

Total Number of Atoms: 30
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O01 O O01 N N N 0 -3.825 -2.45 1.396
2 C03 C C03 N N N 0 -3.735 -1.515 0.319
3 C06 C C06 R N N 0 -2.799 -0.371 0.713
4 O08 O O08 N N N 0 -1.435 -0.84 0.787
5 C09 C C09 R N N 0 -2.784 0.714 -0.387
6 O11 O O11 N N N 0 -3.657 1.791 -0.039
7 C13 C C13 N N N 0 -1.316 1.195 -0.419
8 F14 F F14 N N N 0 -0.749 0.956 -1.675
9 F15 F F15 N N N 0 -1.239 2.555 -0.099
10 C16 C C16 R N N 0 -0.618 0.344 0.665
11 N18 N N18 N N N 0 0.737 -0.013 0.239
12 C19 C C19 N N N 0 0.904 -0.758 -0.866
13 O20 O O20 N N N 0 -0.076 -1.12 -1.488
14 N21 N N21 N N N 0 2.124 -1.115 -1.305
15 C23 C C23 N N N 0 3.229 -0.727 -0.635
16 O24 O O24 N N N 0 4.337 -1.046 -1.027
17 C25 C C25 N N N 0 3.069 0.089 0.578
18 C26 C C26 N N N 0 1.804 0.423 0.97
19 C28 C C28 N N N 0 4.21 0.53 1.322
20 C29 C C29 N N N 0 5.145 0.892 1.933
21 H1 H H1 N N N 0 -4.404 -3.203 1.216
22 H2 H H2 N N N 0 -3.343 -2.017 -0.566
23 H3 H H3 N N N 0 -4.726 -1.116 0.101
24 H4 H H4 N N N 0 -3.106 0.059 1.666
25 H5 H H5 N N N 0 -3.067 0.287 -1.349
26 H6 H H6 N N N 0 -3.686 2.501 -0.695
27 H7 H H7 N N N 0 -0.589 0.884 1.611
28 H8 H H8 N N N 0 2.209 -1.653 -2.107
29 H9 H H9 N N N 0 1.649 1.021 1.855
30 H10 H H10 N N N 0 5.982 1.215 2.478



F2U : Chemical Bonds

Total Number of Bonds: 31
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C29 C28 C C trip 1.17 N N
2 C28 C25 C C sing 1.43 N N
3 C25 C26 C C doub 1.37 N N
4 C25 C23 C C sing 1.47 N N
5 O24 C23 O C doub 1.22 N N
6 C03 O01 C O sing 1.43 N N
7 C03 C06 C C sing 1.53 N N
8 C26 N18 C N sing 1.36 N N
9 C23 N21 C N sing 1.35 N N
10 O08 C06 O C sing 1.44 N N
11 O08 C16 O C sing 1.44 N N
12 C06 C09 C C sing 1.55 N N
13 N18 C16 N C sing 1.46 N N
14 N18 C19 N C sing 1.34 N N
15 N21 C19 N C sing 1.34 N N
16 C16 C13 C C sing 1.54 N N
17 C19 O20 C O doub 1.22 N N
18 C09 C13 C C sing 1.55 N N
19 C09 O11 C O sing 1.43 N N
20 F14 C13 F C sing 1.4 N N
21 C13 F15 C F sing 1.4 N N
22 O01 H1 O H sing 0.97 N N
23 C03 H2 C H sing 1.09 N N
24 C03 H3 C H sing 1.09 N N
25 C06 H4 C H sing 1.09 N N
26 C09 H5 C H sing 1.09 N N
27 O11 H6 O H sing 0.97 N N
28 C16 H7 C H sing 1.09 N N
29 N21 H8 N H sing 0.97 N N
30 C26 H9 C H sing 1.08 N N
31 C29 H10 C H sing 1.05 N N



F2U : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
F2U 4oql Open in New Window Bound ligand 2 1