Chemical Components in the PDB

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FDG : Summary

Code

FDG

One-letter code

G

Molecule name

2-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-7,9-dihydro-1H-purine-6,8-dione

Systematic names

ProgramVersionName
ACDLabs 12.01 2-amino-9-(2-deoxy-2-fluoro-5-O-phosphono-beta-D-arabinofuranosyl)-7,9-dihydro-1H-purine-6,8-dione
OpenEye OEToolkits 1.7.0 [(2R,3R,4S,5R)-5-(2-azanyl-6,8-dioxo-1,7-dihydropurin-9-yl)-4-fluoro-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H13 F N5 O8 P

Formal charge

0

Molecular weight

381.211 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC3OC(N2C(=O)NC1=C2N=C(N)NC1=O)C(F)C3O
SMILES CACTVS 3.370 NC1=NC2=C(NC(=O)N2[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3F)C(=O)N1
SMILES OpenEye OEToolkits 1.7.0 C(C1C(C(C(O1)N2C3=C(C(=O)NC(=N3)N)NC2=O)F)O)OP(=O)(O)O
Canonical SMILES CACTVS 3.370 NC1=NC2=C(NC(=O)N2[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@@H]3F)C(=O)N1
Canonical SMILES OpenEye OEToolkits 1.7.0 C([C@@H]1[C@H]([C@@H]([C@@H](O1)N2C3=C(C(=O)NC(=N3)N)NC2=O)F)O)OP(=O)(O)O

IUPAC InChI

InChI=1S/C10H13FN5O8P/c11-3-5(17)2(1-23-25(20,21)22)24-8(3)16-6-4(13-10(16)19)7(18)15-9(12)14-6/h2-3,5,8,17H,1H2,(H,13,19)(H2,20,21,22)(H3,12,14,15,18)/t2-,3+,5-,8-/m1/s1

IUPAC InChI key

UPQKRMLTATYYQE-HFZKREBBSA-N
FDG

wwPDB Information

Atom count

38 (25 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DG

Defined at

2010-01-06

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



FDG : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 P P P N N N 0 4.954 -1.24 -0.031
2 N1 N N1 N N N 0 -5.318 -1.235 -0.469
3 C2 C C2 N N N 0 -4.601 -0.85 -1.56
4 N2 N N2 N N N 0 -5.158 -0.982 -2.807
5 N3 N N3 N N N 0 -3.386 -0.357 -1.45
6 C4 C C4 N N N 0 -2.805 -0.212 -0.254
7 C5 C C5 N N N 0 -3.494 -0.589 0.893
8 C6 C C6 N N N 0 -4.788 -1.114 0.768
9 O6 O O6 N N N 0 -5.421 -1.455 1.755
10 N7 N N7 N N N 0 -2.653 -0.327 1.978
11 C8 C C8 N N N 0 -1.504 0.186 1.496
12 O8 O O8 N N N 0 -0.549 0.527 2.169
13 N9 N N9 N N N 0 -1.576 0.264 0.154
14 C1' C C1' R N N 0 -0.522 0.77 -0.729
15 C2' C C2' S N N 0 -0.29 2.27 -0.462
16 F2' F F2' N N N 0 -1.103 2.712 0.588
17 C3' C C3' R N N 0 1.203 2.358 -0.065
18 O3' O O3' N N N 0 1.822 3.502 -0.658
19 C4' C C4' R N N 0 1.776 1.048 -0.662
20 O4' O O4' N N N 0 0.714 0.091 -0.454
21 C5' C C5' N N N 0 3.04 0.621 0.088
22 O5' O O5' N N N 0 3.611 -0.521 -0.553
23 OP1 O OP1 N N N 0 4.791 -1.616 1.391
24 OP3 O OP3 N N Y 0 5.231 -2.562 -0.908
25 HN1 H HN1 N N N 0 -6.213 -1.592 -0.579
26 HN2 H HN2 N N N 0 -6.053 -1.344 -2.902
27 HN2A H HN2A N N N 0 -4.658 -0.712 -3.593
28 HN7 H HN7 N N N 0 -2.859 -0.487 2.912
29 H1' H H1' N N N 0 -0.807 0.619 -1.771
30 H2' H H2' N N N 0 -0.483 2.853 -1.363
31 H3' H H3' N N N 0 1.317 2.375 1.019
32 HO3' H HO3' N N Y 0 1.436 4.345 -0.384
33 H4' H H4' N N N 0 1.982 1.168 -1.726
34 H5' H H5' N N N 0 3.76 1.439 0.081
35 H5'A H H5'A N N N 0 2.784 0.37 1.117
36 OP2 O OP2 N N N 0 6.197 -0.227 -0.179
37 HOP3 H HOP3 N N N 0 6.026 -3.046 -0.647
38 HOP2 H HOP2 N N N 0 6.363 0.062 -1.087



FDG : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O5' P O sing 1.61 N N
2 P OP1 P O doub 1.48 N N
3 P OP2 P O sing 1.61 N N
4 N1 C2 N C sing 1.36 N N
5 N1 C6 N C sing 1.35 N N
6 N1 HN1 N H sing 0.97 N N
7 C2 N2 C N sing 1.37 N N
8 C2 N3 C N doub 1.32 N N
9 N2 HN2 N H sing 0.97 N N
10 N2 HN2A N H sing 0.97 N N
11 N3 C4 N C sing 1.34 N N
12 C4 C5 C C doub 1.39 N N
13 C4 N9 C N sing 1.38 N N
14 C5 C6 C C sing 1.4 N N
15 C5 N7 C N sing 1.4 N N
16 C6 O6 C O doub 1.22 N N
17 N7 C8 N C sing 1.35 N N
18 N7 HN7 N H sing 0.97 N N
19 C8 O8 C O doub 1.22 N N
20 C8 N9 C N sing 1.35 N N
21 N9 C1' N C sing 1.47 N N
22 C1' C2' C C sing 1.54 N N
23 C1' O4' C O sing 1.44 N N
24 C1' H1' C H sing 1.09 N N
25 C2' F2' C F sing 1.4 N N
26 C2' C3' C C sing 1.55 N N
27 C2' H2' C H sing 1.09 N N
28 C3' O3' C O sing 1.43 N N
29 C3' C4' C C sing 1.55 N N
30 C3' H3' C H sing 1.09 N N
31 O3' HO3' O H sing 0.97 N N
32 C4' O4' C O sing 1.44 N N
33 C4' C5' C C sing 1.53 N N
34 C4' H4' C H sing 1.09 N N
35 C5' O5' C O sing 1.43 N N
36 C5' H5' C H sing 1.09 N N
37 C5' H5'A C H sing 1.09 N N
38 P OP3 P O sing 1.61 N N
39 OP3 HOP3 O H sing 0.97 N N
40 OP2 HOP2 O H sing 0.97 N N



FDG : Used in PDB Entries

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