Chemical Components in the PDB

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GFH : Summary

Code

GFH

One-letter code

X

Molecule name

2'-DEOXY-5'-O-[(R)-{[(R)-[(R)-FLUORO(PHOSPHONO)METHYL](HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]GUANOSINE

Systematic names

ProgramVersionName
ACDLabs 10.04 2'-deoxy-5'-O-[(R)-{[(R)-[(R)-fluoro(phosphono)methyl](hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]guanosine
OpenEye OEToolkits 1.5.0 [(R)-[[[(2R,3S,5R)-5-(2-amino-6-oxo-1H-purin-9-yl)-3-hydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]-fluoro-methyl]phosphonic acid

Formula

C11 H17 F N5 O12 P3

Formal charge

0

Molecular weight

523.199 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 FC(P(=O)(O)O)P(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c2N=C(N)NC1=O)CC3O
SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)[CH](F)[P](O)(O)=O)O3
SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1C3CC(C(O3)COP(=O)(O)OP(=O)(C(F)P(=O)(O)O)O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@H]3C[C@H](O)[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)[C@H](F)[P](O)(O)=O)O3
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@@](=O)([C@H](F)P(=O)(O)O)O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C11H17FN5O12P3/c12-10(30(20,21)22)31(23,24)29-32(25,26)27-2-5-4(18)1-6(28-5)17-3-14-7-8(17)15-11(13)16-9(7)19/h3-6,10,18H,1-2H2,(H,23,24)(H,25,26)(H2,20,21,22)(H3,13,15,16,19)/t4-,5+,6+,10+/m0/s1

IUPAC InChI key

PVDLZOAYDIZEDJ-AVAJSQPUSA-N
GFH

wwPDB Information

Atom count

49 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-06-01

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



GFH : Atoms of Molecule

Total Number of Atoms: 49
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 -3.641 -0.809 0.559
2 C2 C C2 N N N 0 -7.48 1.351 1.365
3 C2' C C2' N N N 0 -4.106 -2.277 0.43
4 C3' C C3' S N N 0 -2.792 -3.09 0.445
5 C3B C C3B R N N 0 4.987 1.362 0.715
6 C4 C C4 N Y N 0 -5.651 0.663 0.133
7 C4' C C4' R N N 0 -1.688 -2.017 0.581
8 C5 C C5 N Y N 0 -6.1 1.4 -0.969
9 C5' C C5' N N N 0 -0.463 -2.405 -0.249
10 C6 C C6 N N N 0 -7.305 2.131 -0.85
11 C8 C C8 N Y N 0 -4.245 0.441 -1.549
12 F3B F F3B N N N 0 4.326 2.442 0.119
13 H1' H H1' N N N 0 -3.665 -0.494 1.602
14 H2'1 H 1H2' N N N 0 -4.736 -2.554 1.275
15 H2'2 H 2H2' N N N 0 -4.637 -2.428 -0.51
16 H3' H H3' N N N 0 -2.674 -3.642 -0.487
17 H3B H H3B N N N 0 4.665 1.267 1.752
18 H4' H H4' N N N 0 -1.412 -1.889 1.628
19 H5'1 H 1H5' N N N 0 -0.726 -2.404 -1.307
20 H5'2 H 2H5' N N N 0 -0.128 -3.4 0.041
21 H8 H H8 N N N 0 -3.392 0.134 -2.137
22 HN1 H HN1 N N N 0 -8.796 2.58 0.433
23 HN21 H 1HN2 N N N 0 -7.84 0.806 3.296
24 HN22 H 2HN2 N N N 0 -9.002 1.824 2.636
25 HO1A H HO1A N N N 0 1.473 -0.501 -2.565
26 HO1G H HO1G N N N 0 6.844 2.518 -1.347
27 HO2B H HO2B N N N 0 5.108 -1.556 1.422
28 HO2G H HO2G N N N 0 8.083 3.213 1.472
29 HO3' H HO3' N N N 0 -3.439 -4.674 1.528
30 N1 N N1 N N N 0 -7.968 2.087 0.327
31 N2 N N2 N N N 0 -8.175 1.324 2.548
32 N3 N N3 N N N 0 -6.362 0.667 1.267
33 N7 N N7 N Y N 0 -5.2 1.22 -1.966
34 N9 N N9 N Y N 0 -4.483 0.066 -0.259
35 O1A O O1A N N N 0 1.855 -1.355 -2.318
36 O1B O O1B N N N 0 5.023 -0.039 -1.598
37 O1G O O1G N N N 0 7.262 1.788 -0.871
38 O2A O O2A N N N 0 2.616 -2.894 -0.468
39 O2B O O2B N N N 0 5.346 -1.411 0.496
40 O2G O O2G N N N 0 7.141 2.999 1.46
41 O3' O O3' N N N 0 -2.766 -3.98 1.563
42 O3A O O3A N N N 0 2.996 -0.42 -0.142
43 O3G O O3G N N N 0 7.485 0.504 1.291
44 O4' O O4' N N N 0 -2.284 -0.807 0.064
45 O5' O O5' N N N 0 0.586 -1.462 -0.018
46 O6 O O6 N N N 0 -7.733 2.786 -1.784
47 PA P PA R N N 0 2.026 -1.562 -0.731
48 PB P PB R N N 0 4.586 -0.169 -0.19
49 PG P PG N N N 0 6.787 1.647 0.661



GFH : Chemical Bonds

Total Number of Bonds: 51
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 PA O5' P O sing 1.61 N N
2 PA O3A P O sing 1.61 N N
3 PA O2A P O doub 1.48 N N
4 PA O1A P O sing 1.61 N N
5 O1A HO1A O H sing 0.97 N N
6 O3A PB O P sing 1.61 N N
7 O5' C5' O C sing 1.43 N N
8 PB O1B P O doub 1.48 N N
9 PB O2B P O sing 1.61 N N
10 PB C3B P C sing 1.82 N N
11 O2B HO2B O H sing 0.97 N N
12 C3B F3B C F sing 1.4 N N
13 C3B PG C P sing 1.82 N N
14 C3B H3B C H sing 1.09 N N
15 PG O3G P O doub 1.48 N N
16 PG O1G P O sing 1.61 N N
17 PG O2G P O sing 1.61 N N
18 O1G HO1G O H sing 0.97 N N
19 O2G HO2G O H sing 0.97 N N
20 C5' C4' C C sing 1.53 N N
21 C5' H5'1 C H sing 1.09 N N
22 C5' H5'2 C H sing 1.09 N N
23 C4' C3' C C sing 1.55 N N
24 C4' O4' C O sing 1.44 N N
25 C4' H4' C H sing 1.09 N N
26 O4' C1' O C sing 1.44 N N
27 C1' C2' C C sing 1.55 N N
28 C1' N9 C N sing 1.46 N N
29 C1' H1' C H sing 1.09 N N
30 N9 C4 N C sing 1.37 N Y
31 N9 C8 N C sing 1.36 N Y
32 C4 N3 C N sing 1.34 N N
33 C4 C5 C C doub 1.4 N Y
34 N3 C2 N C doub 1.31 N N
35 C2 N2 C N sing 1.37 N N
36 C2 N1 C N sing 1.36 N N
37 N2 HN21 N H sing 0.97 N N
38 N2 HN22 N H sing 0.97 N N
39 N1 C6 N C sing 1.35 N N
40 N1 HN1 N H sing 0.97 N N
41 C6 O6 C O doub 1.22 N N
42 C6 C5 C C sing 1.41 N N
43 C5 N7 C N sing 1.36 N Y
44 N7 C8 N C doub 1.3 N Y
45 C8 H8 C H sing 1.08 N N
46 C2' C3' C C sing 1.55 N N
47 C2' H2'1 C H sing 1.09 N N
48 C2' H2'2 C H sing 1.09 N N
49 C3' O3' C O sing 1.43 N N
50 C3' H3' C H sing 1.09 N N
51 O3' HO3' O H sing 0.97 N N



GFH : Used in PDB Entries

Total Number of PDB Entries: 5
Ligand Code PDB Entry ID Type Total Distinct
GFH 2pxi Open in New Window Bound ligand 1 1
GFH 4do9 Open in New Window Bound ligand 1 1
GFH 6nks Open in New Window Bound ligand 1 1
GFH 6nkv Open in New Window Bound ligand 1 1
GFH 6nky Open in New Window Bound ligand 1 1