Chemical Components in the PDB

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GGZ : Summary

Code

GGZ

One-letter code

X

Molecule name

(2S,3AR,4R,6R,6AR)-4-(6-AMINO-9H-PURIN-9-YL)-6-({[(R)-HYDROXY(SULFOOXY)PHOSPHORYL]OXY}METHYL)TETRAHYDROFURO[3,4-D][1,3,2]DIOXAPHOSPHOL-2-OL 2-OXIDE

Systematic names

ProgramVersionName
ACDLabs 10.04 (2S,3aR,4R,6R,6aR)-4-(6-amino-9H-purin-9-yl)-6-({[(R)-hydroxy(sulfooxy)phosphoryl]oxy}methyl)tetrahydrofuro[3,4-d][1,3,2]dioxaphosphol-2-ol 2-oxide
OpenEye OEToolkits 1.5.0 [(1R,2R,4R,5R,7S)-4-(6-aminopurin-9-yl)-7-hydroxy-7-oxo-3,6,8-trioxa-7$l^{5}-phosphabicyclo[3.3.0]octan-2-yl]methyl sulfo hydrogen phosphate

Formula

C10 H13 N5 O12 P2 S

Formal charge

0

Molecular weight

489.249 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P3(OC4C(OC(n1c2ncnc(N)c2nc1)C4O3)COP(=O)(O)OS(=O)(=O)O)O
SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[S](O)(=O)=O)[CH]4O[P](O)(=O)O[CH]34
SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)C3C4C(C(O3)COP(=O)(O)OS(=O)(=O)O)OP(=O)(O4)O)N
Canonical SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[S](O)(=O)=O)[C@H]4O[P@@](O)(=O)O[C@@H]34
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@H]4[C@@H]([C@H](O3)CO[P@@](=O)(O)OS(=O)(=O)O)O[P@@](=O)(O4)O)N

IUPAC InChI

InChI=1S/C10H13N5O12P2S/c11-8-5-9(13-2-12-8)15(3-14-5)10-7-6(25-29(18,19)26-7)4(24-10)1-23-28(16,17)27-30(20,21)22/h2-4,6-7,10H,1H2,(H,16,17)(H,18,19)(H2,11,12,13)(H,20,21,22)/t4-,6-,7-,10-/m1/s1

IUPAC InChI key

BOTWXJFMSRDLBQ-KQYNXXCUSA-N
GGZ

wwPDB Information

Atom count

43 (30 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-04-05

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



GGZ : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C2 N Y N 0 2.0 1.98 -3.099
2 C4 C C4 N Y N 0 2.272 1.694 -0.923
3 C5 C C5 N Y N 0 2.579 3.031 -0.728
4 C6 C C6 N Y N 0 2.576 3.847 -1.855
5 C8 C C8 N N N 0 2.685 2.121 1.196
6 N1 N N1 N Y N 0 2.28 3.305 -3.061
7 O3P O O3P N N N 0 -2.1 -2.246 0.247
8 P1 P P1 N N N 0 -0.622 -2.846 0.504
9 O2' O O2* N N N 0 0.175 -1.634 1.233
10 O1P O O1P N N N 0 -0.57 -4.178 1.189
11 O3' O O3* N N N 0 0.09 -2.76 -0.953
12 C3' C C3* N N N 0 1.038 -1.695 -0.957
13 C4' C C4* N N N 0 2.438 -2.191 -0.636
14 C5' C C5* N N N 0 3.219 -2.615 -1.866
15 O5' O O5* N N N 0 4.506 -3.047 -1.46
16 P2 P P2 N N N 0 5.802 -2.27 -2.042
17 O4P O O4P N N N 0 7.142 -2.767 -1.581
18 O5P O O5P N N N 0 5.592 -2.322 -3.647
19 O6P O O6P N N N 0 5.448 -0.73 -1.683
20 S2 S S2 N N N 0 6.48 0.369 -2.31
21 OS3 O OS3 N N N 0 6.469 0.253 -3.756
22 OS2 O OS2 N N N 0 5.766 1.784 -1.928
23 OS1 O OS1 N N N 0 7.728 0.299 -1.572
24 C2' C C2* N N N 0 0.735 -0.78 0.222
25 C1' C C1* N N N 0 2.104 -0.277 0.656
26 O4' O O4* N N N 0 3.1 -1.09 0.003
27 N9 N N9 N N N 0 2.344 1.125 0.318
28 N7 N N7 N N N 0 2.834 3.283 0.596
29 N6 N N6 N N N 0 2.876 5.217 -1.75
30 N3 N N3 N Y N 0 1.971 1.091 -2.082
31 H2 H H2 N N N 0 1.767 1.579 -4.079
32 H8 H H8 N N N 0 2.809 1.939 2.255
33 HO3P H HO3P N N N 0 -2.836 -2.538 0.826
34 H3' H H3* N N N 0 1.001 -1.148 -1.905
35 H4' H H4* N N N 0 2.416 -3.031 0.069
36 H5'1 H 1H5* N N N 0 3.325 -1.773 -2.553
37 H5'2 H 2H5* N N N 0 2.708 -3.436 -2.372
38 HO5P H HO5P N N N 0 6.301 -1.975 -4.229
39 HOS2 H HOS2 N N N 0 5.454 1.861 -0.996
40 H2' H H2* N N N 0 0.002 0.002 -0.001
41 H1' H H1* N N N 0 2.255 -0.346 1.738
42 HN61 H 1HN6 N N N 0 3.501 5.531 -1.032
43 HN62 H 2HN6 N N N 0 2.39 5.873 -2.331



GGZ : Chemical Bonds

Total Number of Bonds: 46
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 N3 C N doub 1.35 N Y
2 C2 N1 C N sing 1.35 N Y
3 C2 H2 C H sing 1.08 N N
4 C4 N9 C N sing 1.37 N N
5 C4 C5 C C doub 1.39 N Y
6 C4 N3 C N sing 1.34 N Y
7 C5 N7 C N sing 1.37 N N
8 C5 C6 C C sing 1.39 N Y
9 C6 N6 C N sing 1.41 N N
10 C6 N1 C N doub 1.35 N Y
11 C8 N7 C N doub 1.32 N N
12 C8 N9 C N sing 1.37 N N
13 C8 H8 C H sing 1.08 N N
14 O3P P1 O P sing 1.62 N N
15 O3P HO3P O H sing 0.98 N N
16 P1 O3' P O sing 1.62 N N
17 P1 O1P P O doub 1.5 N N
18 P1 O2' P O sing 1.62 N N
19 O2' C2' O C sing 1.44 N N
20 O3' C3' O C sing 1.43 N N
21 C3' C4' C C sing 1.52 N N
22 C3' C2' C C sing 1.52 N N
23 C3' H3' C H sing 1.1 N N
24 C4' O4' C O sing 1.43 N N
25 C4' C5' C C sing 1.52 N N
26 C4' H4' C H sing 1.1 N N
27 C5' O5' C O sing 1.42 N N
28 C5' H5'1 C H sing 1.09 N N
29 C5' H5'2 C H sing 1.09 N N
30 O5' P2 O P sing 1.62 N N
31 P2 O4P P O doub 1.5 N N
32 P2 O6P P O sing 1.62 N N
33 P2 O5P P O sing 1.62 N N
34 O5P HO5P O H sing 0.98 N N
35 O6P S2 O S sing 1.63 N N
36 S2 OS1 S O doub 1.45 N N
37 S2 OS3 S O doub 1.45 N N
38 S2 OS2 S O sing 1.63 N N
39 OS2 HOS2 O H sing 0.99 N N
40 C2' C1' C C sing 1.52 N N
41 C2' H2' C H sing 1.09 N N
42 C1' O4' C O sing 1.44 N N
43 C1' N9 C N sing 1.46 N N
44 C1' H1' C H sing 1.09 N N
45 N6 HN61 N H sing 1.0 N N
46 N6 HN62 N H sing 1.0 N N



GGZ : Used in PDB Entries

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