Chemical Components in the PDB

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8AG : Summary

Code

8AG

One-letter code

G

Molecule name

8-[ACETYL(ANTHRACEN-2-YL)AMINO]-2'-DEOXYGUANOSINE 5'-(DIHYDROGEN PHOSPHATE)

Systematic names

ProgramVersionName
ACDLabs 10.04 8-[acetyl(anthracen-2-yl)amino]-2'-deoxyguanosine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.6.1 [(2R,3S,5R)-5-[2-amino-8-(anthracen-2-yl-ethanoyl-amino)-6-oxo-7,8-dihydro-1H-purin-9-yl]-3-hydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C26 H27 N6 O8 P

Formal charge

0

Molecular weight

582.502 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(N(c3cc2cc1ccccc1cc2cc3)C5N(C=4N=C(N)NC(=O)C=4N5)C6OC(C(O)C6)COP(=O)(O)O)C
SMILES CACTVS 3.352 CC(=O)N([CH]1NC2=C(N=C(N)NC2=O)N1[CH]3C[CH](O)[CH](CO[P](O)(O)=O)O3)c4ccc5cc6ccccc6cc5c4
SMILES OpenEye OEToolkits 1.6.1 CC(=O)N(c1ccc2cc3ccccc3cc2c1)C4NC5=C(N4C6CC(C(O6)COP(=O)(O)O)O)N=C(NC5=O)N
Canonical SMILES CACTVS 3.352 CC(=O)N([C@H]1NC2=C(N=C(N)NC2=O)N1[C@H]3C[C@H](O)[C@@H](CO[P](O)(O)=O)O3)c4ccc5cc6ccccc6cc5c4
Canonical SMILES OpenEye OEToolkits 1.6.1 CC(=O)N(c1ccc2cc3ccccc3cc2c1)C4NC5=C(N4[C@H]6C[C@@H]([C@H](O6)COP(=O)(O)O)O)N=C(NC5=O)N

IUPAC InChI

InChI=1S/C26H27N6O8P/c1-13(33)31(18-7-6-16-8-14-4-2-3-5-15(14)9-17(16)10-18)26-28-22-23(29-25(27)30-24(22)35)32(26)21-11-19(34)20(40-21)12-39-41(36,37)38/h2-10,19-21,26,28,34H,11-12H2,1H3,(H2,36,37,38)(H3,27,29,30,35)/t19-,20+,21+,26+/m0/s1

IUPAC InChI key

OCECNASCCDEYBO-GQNXPXPTSA-N
8AG

wwPDB Information

Atom count

68 (41 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

DG

Defined at

2010-06-07

Last modified at

2019-05-03

Status

Released

Obsoleted

Not Assigned



8AG : Atoms of Molecule

Total Number of Atoms: 68
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 -5.689 2.908 1.173
2 O2P O O2P N N N 0 -6.808 3.404 0.341
3 O1P O O1P N N N 0 -5.202 4.074 2.17
4 O3P O O3P N N Y 0 -6.181 1.638 2.032
5 O5' O O5' N N N 0 -4.466 2.47 0.221
6 C5' C C5' N N N 0 -4.607 1.528 -0.844
7 C4' C C4' R N N 0 -3.258 1.342 -1.542
8 O4' O O4' N N N 0 -2.309 0.712 -0.655
9 C3' C C3' S N N 0 -3.384 0.333 -2.712
10 O3' O O3' N N N 0 -3.802 0.99 -3.91
11 C2' C C2' N N N 0 -1.933 -0.19 -2.846
12 C1' C C1' R N N 0 -1.291 0.122 -1.48
13 N9 N N9 N N N 0 -0.806 -1.116 -0.864
14 C4 C C4 N N N 0 -1.587 -2.185 -0.456
15 N3 N N3 N N N 0 -2.916 -2.366 -0.51
16 C2 C C2 N N N 0 -3.474 -3.469 -0.064
17 N2 N N2 N N N 0 -4.837 -3.609 -0.14
18 N1 N N1 N N N 0 -2.732 -4.475 0.472
19 C6 C C6 N N N 0 -1.39 -4.354 0.555
20 O6 O O6 N N N 0 -0.714 -5.252 1.034
21 C5 C C5 N N N 0 -0.787 -3.18 0.081
22 N7 N N7 N N N 0 0.567 -2.782 0.038
23 C8 C C8 S N N 0 0.594 -1.447 -0.575
24 N29 N N29 N N N 0 1.161 -0.474 0.362
25 C30 C C30 N N N 0 0.348 0.349 1.054
26 C45 C C45 N N N 0 0.927 1.312 2.057
27 O44 O O44 N N N 0 -0.85 0.313 0.869
28 C32 C C32 N Y N 0 2.546 -0.398 0.539
29 C31 C C31 N Y N 0 3.159 -1.212 1.5
30 C36 C C36 N Y N 0 4.498 -1.18 1.712
31 C35 C C35 N Y N 0 5.305 -0.306 0.95
32 C34 C C34 N Y N 0 4.667 0.547 -0.058
33 C33 C C33 N Y N 0 3.27 0.462 -0.234
34 C1 C C1 N Y N 0 6.683 -0.25 1.145
35 C39 C C39 N Y N 0 7.452 0.623 0.377
36 C38 C C38 N Y N 0 6.814 1.477 -0.631
37 C37 C C37 N Y N 0 5.436 1.42 -0.826
38 C43 C C43 N Y N 0 8.851 0.706 0.549
39 C42 C C42 N Y N 0 9.569 1.567 -0.216
40 C40 C C40 N Y N 0 7.623 2.349 -1.391
41 C41 C C41 N Y N 0 8.962 2.38 -1.175
42 H1P H H1P N N N 0 -5.889 4.387 2.774
43 H5'1 H H5'1 N N N 0 -4.942 0.572 -0.441
44 H5'2 H H5'2 N N N 0 -5.339 1.897 -1.561
45 H4' H H4' N N N 0 -2.876 2.299 -1.897
46 H3' H H3' N N N 0 -4.067 -0.477 -2.456
47 H1' H H1' N N N 0 -0.466 0.822 -1.61
48 H2'1 H H2'1 N N N 0 -1.93 -1.264 -3.033
49 H2'2 H H2'2 N N N 0 -1.409 0.338 -3.643
50 H21N H H21N N N N 0 -5.377 -2.898 -0.521
51 H451 H H451 N N N 0 1.244 2.222 1.547
52 H22N H H22N N N N 0 -5.261 -4.418 0.186
53 H1 H H1 N N N 0 -3.167 -5.28 0.795
54 H7 H H7 N N N 0 1.331 -3.292 0.35
55 H452 H H452 N N N 0 0.171 1.559 2.803
56 H453 H H453 N N N 0 1.786 0.854 2.548
57 H31 H H31 N N N 0 2.549 -1.883 2.088
58 HA H HA N N N 0 7.153 -0.878 1.887
59 H33 H H33 N N N 0 2.776 1.077 -0.971
60 H36 H H36 N N N 0 4.945 -1.818 2.461
61 H37 H H37 N N N 0 4.966 2.049 -1.568
62 H43 H H43 N N N 0 9.346 0.089 1.284
63 H40 H H40 N N N 0 7.178 2.988 -2.139
64 H42 H H42 N N N 0 10.639 1.626 -0.079
65 H3A H H3A N N N 0 -3.895 0.401 -4.67
66 H41 H H41 N N N 0 9.575 3.05 -1.76
67 H88 H H88 N N N 0 1.175 -1.466 -1.497
68 H3P H H3P N N N 0 -5.497 1.26 2.602



8AG : Chemical Bonds

Total Number of Bonds: 73
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 P O2P P O doub 1.48 N N
2 P O1P P O sing 1.61 N N
3 P O5' P O sing 1.61 N N
4 P O3P P O sing 1.61 N N
5 O5' C5' O C sing 1.43 N N
6 C5' C4' C C sing 1.53 N N
7 C4' O4' C O sing 1.44 N N
8 C4' C3' C C sing 1.55 N N
9 O4' C1' O C sing 1.44 N N
10 C3' O3' C O sing 1.43 N N
11 C3' C2' C C sing 1.55 N N
12 O3' H3A O H sing 0.97 N N
13 C2' C1' C C sing 1.54 N N
14 C1' N9 C N sing 1.47 N N
15 N9 C4 N C sing 1.39 N N
16 N9 C8 N C sing 1.47 N N
17 C4 N3 C N sing 1.34 N N
18 C4 C5 C C doub 1.39 N N
19 N3 C2 N C doub 1.31 N N
20 C2 N2 C N sing 1.37 N N
21 C2 N1 C N sing 1.36 N N
22 N1 C6 N C sing 1.35 N N
23 C6 O6 C O doub 1.22 N N
24 C6 C5 C C sing 1.4 N N
25 C5 N7 C N sing 1.41 N N
26 N7 C8 N C sing 1.47 N N
27 C8 N29 C N sing 1.46 N N
28 N29 C30 N C sing 1.35 N N
29 N29 C32 N C sing 1.4 N N
30 C30 C45 C C sing 1.51 N N
31 C30 O44 C O doub 1.21 N N
32 C32 C31 C C sing 1.4 N Y
33 C32 C33 C C doub 1.36 N Y
34 C31 C36 C C doub 1.36 N Y
35 C36 C35 C C sing 1.41 N Y
36 C35 C34 C C sing 1.47 N Y
37 C35 C1 C C doub 1.39 N Y
38 C34 C33 C C sing 1.41 N Y
39 C34 C37 C C doub 1.39 N Y
40 C1 C39 C C sing 1.39 N Y
41 C39 C38 C C doub 1.47 N Y
42 C39 C43 C C sing 1.41 N Y
43 C38 C37 C C sing 1.39 N Y
44 C38 C40 C C sing 1.41 N Y
45 C40 C41 C C doub 1.36 N Y
46 C43 C42 C C doub 1.36 N Y
47 C42 C41 C C sing 1.4 N Y
48 O1P H1P O H sing 0.97 N N
49 C5' H5'1 C H sing 1.09 N N
50 C5' H5'2 C H sing 1.09 N N
51 C4' H4' C H sing 1.09 N N
52 C3' H3' C H sing 1.09 N N
53 C1' H1' C H sing 1.09 N N
54 C2' H2'1 C H sing 1.09 N N
55 C2' H2'2 C H sing 1.09 N N
56 N2 H21N N H sing 0.97 N N
57 N2 H22N N H sing 0.97 N N
58 N1 H1 N H sing 0.97 N N
59 N7 H7 N H sing 0.97 N N
60 C45 H451 C H sing 1.09 N N
61 C45 H452 C H sing 1.09 N N
62 C45 H453 C H sing 1.09 N N
63 C31 H31 C H sing 1.08 N N
64 C33 H33 C H sing 1.08 N N
65 C36 H36 C H sing 1.08 N N
66 C1 HA C H sing 1.08 N N
67 C37 H37 C H sing 1.08 N N
68 C43 H43 C H sing 1.08 N N
69 C40 H40 C H sing 1.08 N N
70 C42 H42 C H sing 1.08 N N
71 C41 H41 C H sing 1.08 N N
72 C8 H88 C H sing 1.09 N N
73 O3P H3P O H sing 0.97 N N



8AG : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
8AG 2xgq Open in New Window Polymer component 2 1