Chemical Components in the PDB

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GP5 : Summary

Code

GP5

One-letter code

X

Molecule name

DIGUANOSINE-PENTAPHOSPHATE

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.5.0 [[[[[(2S,3R,4S,5S)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methoxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl]oxy-hydroxy-phosphoryl] [(2S,3R,4S,5S)-5-(2-amino-6-oxo-1H-purin-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl hydrogen phosphate

Formula

C20 H29 N10 O24 P5

Formal charge

0

Molecular weight

948.366 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)O[P](O)(=O)OC[CH]4O[CH]([CH](O)[CH]4O)n5cnc6C(=O)NC(=Nc56)N)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OP(=O)(O)OCC4C(C(C(O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N=C(NC2=O)N
Canonical SMILES CACTVS 3.341 NC1=Nc2n(cnc2C(=O)N1)[C@H]3O[C@@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)O[P@@](O)(=O)O[P@](O)(=O)OC[C@H]4O[C@H]([C@H](O)[C@@H]4O)n5cnc6C(=O)NC(=Nc56)N)[C@H](O)[C@@H]3O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc2c(n1[C@@H]3[C@H]([C@H]([C@@H](O3)CO[P@@](=O)(O)O[P@@](=O)(O)OP(=O)(O)O[P@](=O)(O)O[P@@](=O)(O)OC[C@@H]4[C@H]([C@H]([C@@H](O4)n5cnc6c5N=C(NC6=O)N)O)O)O)O)N=C(NC2=O)N

IUPAC InChI

InChI=1S/C20H29N10O24P5/c21-19-25-13-7(15(35)27-19)23-3-29(13)17-11(33)9(31)5(49-17)1-47-55(37,38)51-57(41,42)53-59(45,46)54-58(43,44)52-56(39,40)48-2-6-10(32)12(34)18(50-6)30-4-24-8-14(30)26-20(22)28-16(8)36/h3-6,9-12,17-18,31-34H,1-2H2,(H,37,38)(H,39,40)(H,41,42)(H,43,44)(H,45,46)(H3,21,25,27,35)(H3,22,26,28,36)/t5-,6+,9-,10+,11-,12+,17-,18+

IUPAC InChI key

RELSGTOCAPVUGP-DTFXMBEISA-N
GP5

wwPDB Information

Atom count

88 (59 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-11-09

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



GP5 : Atoms of Molecule

Total Number of Atoms: 88
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O6 O O6 N N N 0 12.193 -5.785 -0.243
2 C6 C C6 N N N 0 12.436 -4.592 -0.315
3 N1 N N1 N N N 0 13.695 -4.154 -0.535
4 C2 C C2 N N N 0 13.956 -2.818 -0.608
5 N2 N N2 N N N 0 15.245 -2.402 -0.826
6 N3 N N3 N N N 0 13.008 -1.917 -0.479
7 C4 C C4 N Y N 0 11.737 -2.276 -0.265
8 C5 C C5 N Y N 0 11.405 -3.633 -0.175
9 N7 N N7 N Y N 0 10.07 -3.708 0.042
10 C8 C C8 N Y N 0 9.573 -2.506 0.089
11 N9 N N9 N Y N 0 10.566 -1.588 -0.095
12 C1' C C1* S N N 0 10.408 -0.132 -0.109
13 O4' O O4* N N N 0 9.04 0.228 -0.399
14 C2' C C2* S N N 0 10.649 0.457 1.305
15 O2' O O2* N N N 0 12.037 0.712 1.527
16 C3' C C3* R N N 0 9.845 1.781 1.244
17 O3' O O3* N N N 0 10.713 2.879 0.954
18 C4' C C4* S N N 0 8.845 1.565 0.092
19 C5' C C5* N N N 0 7.413 1.727 0.606
20 O5' O O5* N N N 0 6.499 1.625 -0.489
21 PCC P PCC R N N 0 5.02 1.804 0.121
22 OAN O OAN N N N 0 4.81 0.815 1.202
23 OAE O OAE N N N 0 4.861 3.291 0.716
24 OBG O OBG N N N 0 3.929 1.57 -1.04
25 PCE P PCE S N N 0 2.509 1.365 -0.309
26 OAP O OAP N N N 0 2.347 2.386 0.75
27 OAG O OAG N N N 0 2.451 -0.104 0.348
28 OBI O OBI N N N 0 1.324 1.517 -1.388
29 PCG P PCG R N N 0 -0.02 1.834 -0.56
30 OAR O OAR N N N 0 -0.049 1.011 0.669
31 OAI O OAI N N N 0 -0.05 3.394 -0.162
32 OBJ O OBJ N N N 0 -1.304 1.488 -1.469
33 PCF P PCF R N N 0 -2.574 1.44 -0.48
34 OAQ O OAQ N N N 0 -2.53 2.601 0.437
35 OAH O OAH N N N 0 -2.535 0.077 0.377
36 OBH O OBH N N N 0 -3.93 1.491 -1.346
37 PCD P PCD S N N 0 -5.101 1.969 -0.35
38 OAO O OAO N N N 0 -4.922 1.322 0.969
39 OAF O OAF N N N 0 -5.036 3.568 -0.176
40 OBD O OBD N N N 0 -6.53 1.553 -0.962
41 CAV C CAV N N N 0 -7.514 1.896 0.016
42 CBZ C CBZ R N N 0 -8.903 1.525 -0.507
43 OBF O OBF N N N 0 -9.018 0.096 -0.619
44 CBV C CBV S N N 0 -9.981 1.997 0.489
45 OAL O OAL N N N 0 -10.874 2.923 -0.133
46 CBW C CBW R N N 0 -10.732 0.696 0.876
47 OAM O OAM N N N 0 -12.14 0.924 0.951
48 CXB C CXB R N N 0 -10.386 -0.243 -0.308
49 NBY N NBY N Y N 0 -10.491 -1.648 0.095
50 CAT C CAT N Y N 0 -9.488 -2.416 0.61
51 NAX N NAX N Y N 0 -9.932 -3.614 0.856
52 CBP C CBP N Y N 0 -11.242 -3.685 0.516
53 CBR C CBR N Y N 0 -11.614 -2.427 0.031
54 NAZ N NAZ N N N 0 -12.869 -2.221 -0.385
55 CBL C CBL N N N 0 -13.767 -3.18 -0.337
56 NAB N NAB N N N 0 -15.043 -2.921 -0.77
57 NBB N NBB N N N 0 -13.466 -4.425 0.13
58 CBN C CBN N N N 0 -12.218 -4.709 0.562
59 OAD O OAD N N N 0 -11.939 -5.819 0.982
60 HN1 H HN1 N N N 0 14.418 -4.793 -0.634
61 HN21 H 1HN2 N N N 0 15.446 -1.454 -0.884
62 HN22 H 2HN2 N N N 0 15.956 -3.055 -0.919
63 H8 H H8 N N N 0 8.532 -2.271 0.251
64 H1' H H1* N N N 0 11.085 0.32 -0.833
65 H2' H H2* N N N 0 10.249 -0.206 2.072
66 H4' H H4* N N N 0 9.036 2.284 -0.704
67 H2 H H2 N N N 0 12.105 1.16 2.382
68 H3' H H3* N N N 0 9.317 1.951 2.182
69 H1 H H1 N N N 0 11.314 2.966 1.706
70 H5'1 H 1H5* N N N 0 7.197 0.944 1.333
71 H5'2 H 2H5* N N N 0 7.305 2.702 1.08
72 HAE H HAE N N N 0 5.005 3.903 -0.019
73 HAG H HAG N N N 0 2.56 -0.738 -0.374
74 HAI H HAI N N N 0 -0.03 3.894 -0.99
75 HAH H HAH N N N 0 -2.565 -0.653 -0.257
76 HAF H HAF N N N 0 -5.157 3.951 -1.056
77 HAV1 H 1HAV N N N 0 -7.315 1.351 0.938
78 HAV2 H 2HAV N N N 0 -7.474 2.968 0.211
79 HBZ H HBZ N N N 0 -9.069 1.987 -1.48
80 HBV H HBV N N N 0 -9.518 2.446 1.367
81 HAL H HAL N N N 0 -11.557 3.134 0.519
82 HBW H HBW N N N 0 -10.354 0.292 1.815
83 HAM H HAM N N N 0 -12.288 1.512 1.704
84 HXB H HXB N N N 0 -11.035 -0.04 -1.161
85 HAT H HAT N N N 0 -8.476 -2.081 0.786
86 HAB1 H 1HAB N N N 0 -15.716 -3.619 -0.742
87 HAB2 H 2HAB N N N 0 -15.272 -2.04 -1.105
88 HBB H HBB N N N 0 -14.152 -5.111 0.151



GP5 : Chemical Bonds

Total Number of Bonds: 93
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C6 O C doub 1.22 N N
2 C6 N1 C N sing 1.35 N N
3 C6 C5 C C sing 1.42 N N
4 N1 C2 N C sing 1.36 N N
5 N1 HN1 N H sing 0.97 N N
6 C2 N2 C N sing 1.37 N N
7 C2 N3 C N doub 1.31 N N
8 N2 HN21 N H sing 0.97 N N
9 N2 HN22 N H sing 0.97 N N
10 N3 C4 N C sing 1.34 N N
11 C4 C5 C C doub 1.4 N Y
12 C4 N9 C N sing 1.37 N Y
13 C5 N7 C N sing 1.35 N Y
14 N7 C8 N C doub 1.3 N Y
15 C8 N9 C N sing 1.36 N Y
16 C8 H8 C H sing 1.08 N N
17 N9 C1' N C sing 1.46 N N
18 C1' O4' C O sing 1.44 N N
19 C1' C2' C C sing 1.55 N N
20 C1' H1' C H sing 1.09 N N
21 O4' C4' O C sing 1.44 N N
22 C2' O2' C O sing 1.43 N N
23 C2' C3' C C sing 1.55 N N
24 C2' H2' C H sing 1.09 N N
25 O2' H2 O H sing 0.97 N N
26 C3' O3' C O sing 1.43 N N
27 C3' C4' C C sing 1.54 N N
28 C3' H3' C H sing 1.09 N N
29 O3' H1 O H sing 0.97 N N
30 C4' C5' C C sing 1.53 N N
31 C4' H4' C H sing 1.09 N N
32 C5' O5' C O sing 1.43 N N
33 C5' H5'1 C H sing 1.09 N N
34 C5' H5'2 C H sing 1.09 N N
35 O5' PCC O P sing 1.61 N N
36 PCC OAN P O doub 1.48 N N
37 PCC OAE P O sing 1.61 N N
38 PCC OBG P O sing 1.61 N N
39 OAE HAE O H sing 0.97 N N
40 OBG PCE O P sing 1.61 N N
41 PCE OAP P O doub 1.48 N N
42 PCE OAG P O sing 1.61 N N
43 PCE OBI P O sing 1.61 N N
44 OAG HAG O H sing 0.97 N N
45 OBI PCG O P sing 1.61 N N
46 PCG OAR P O doub 1.48 N N
47 PCG OAI P O sing 1.61 N N
48 PCG OBJ P O sing 1.61 N N
49 OAI HAI O H sing 0.97 N N
50 OBJ PCF O P sing 1.61 N N
51 PCF OAQ P O doub 1.48 N N
52 PCF OAH P O sing 1.61 N N
53 PCF OBH P O sing 1.61 N N
54 OAH HAH O H sing 0.97 N N
55 OBH PCD O P sing 1.61 N N
56 PCD OAO P O doub 1.48 N N
57 PCD OAF P O sing 1.61 N N
58 PCD OBD P O sing 1.61 N N
59 OAF HAF O H sing 0.97 N N
60 OBD CAV O C sing 1.43 N N
61 CAV CBZ C C sing 1.53 N N
62 CAV HAV1 C H sing 1.09 N N
63 CAV HAV2 C H sing 1.09 N N
64 CBZ OBF C O sing 1.44 N N
65 CBZ CBV C C sing 1.54 N N
66 CBZ HBZ C H sing 1.09 N N
67 OBF CXB O C sing 1.44 N N
68 CBV OAL C O sing 1.43 N N
69 CBV CBW C C sing 1.55 N N
70 CBV HBV C H sing 1.09 N N
71 OAL HAL O H sing 0.97 N N
72 CBW OAM C O sing 1.43 N N
73 CBW CXB C C sing 1.55 N N
74 CBW HBW C H sing 1.09 N N
75 OAM HAM O H sing 0.97 N N
76 CXB NBY C N sing 1.47 N N
77 CXB HXB C H sing 1.09 N N
78 NBY CAT N C sing 1.36 N Y
79 NBY CBR N C sing 1.37 N Y
80 CAT NAX C N doub 1.3 N Y
81 CAT HAT C H sing 1.08 N N
82 NAX CBP N C sing 1.36 N Y
83 CBP CBR C C doub 1.4 N Y
84 CBP CBN C C sing 1.42 N N
85 CBR NAZ C N sing 1.34 N N
86 NAZ CBL N C doub 1.31 N N
87 CBL NAB C N sing 1.37 N N
88 CBL NBB C N sing 1.36 N N
89 NAB HAB1 N H sing 0.97 N N
90 NAB HAB2 N H sing 0.97 N N
91 NBB CBN N C sing 1.35 N N
92 NBB HBB N H sing 0.97 N N
93 CBN OAD C O doub 1.22 N N



GP5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
GP5 2bbw Open in New Window Bound ligand 2 1