Chemical Components in the PDB

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8AA : Summary

Code

8AA

One-letter code

G

Molecule name

8-[acetyl(anthracen-2-yl)amino]-2'-deoxy-5'-O-(dihydroxyphosphanyl)guanosine

Systematic names

ProgramVersionName
ACDLabs 12.01 8-[acetyl(anthracen-2-yl)amino]-2'-deoxy-5'-O-(dihydroxyphosphanyl)guanosine
OpenEye OEToolkits 1.7.6 [(2R,3S,5R)-5-[8-[anthracen-2-yl(ethanoyl)amino]-2-azanyl-6-oxidanylidene-3H-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphite

Formula

C26 H25 N6 O7 P

Formal charge

0

Molecular weight

564.486 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 P(OCC6C(CC(n5c1NC(=NC(c1nc5N(c4ccc3cc2ccccc2cc3c4)C(C)=O)=O)N)O6)O)(O)O
SMILES CACTVS 3.385 CC(=O)N(c1ccc2cc3ccccc3cc2c1)c4nc5C(=O)N=C(N)Nc5n4[CH]6C[CH](O)[CH](COP(O)O)O6
SMILES OpenEye OEToolkits 1.7.6 CC(=O)N(c1ccc2cc3ccccc3cc2c1)c4nc5c(n4C6CC(C(O6)COP(O)O)O)NC(=NC5=O)N
Canonical SMILES CACTVS 3.385 CC(=O)N(c1ccc2cc3ccccc3cc2c1)c4nc5C(=O)N=C(N)Nc5n4[C@H]6C[C@H](O)[C@@H](COP(O)O)O6
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(=O)N(c1ccc2cc3ccccc3cc2c1)c4nc5c(n4[C@H]6C[C@@H]([C@H](O6)COP(O)O)O)NC(=NC5=O)N

IUPAC InChI

InChI=1S/C26H25N6O7P/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(39-21)12-38-40(36)37/h2-10,19-21,34,36-37H,11-12H2,1H3,(H3,27,29,30,35)/t19-,20+,21+/m0/s1

IUPAC InChI key

RRBSUYWZIMIROG-PWRODBHTSA-N
8AA

wwPDB Information

Atom count

65 (40 without Hydrogen)

Polymer type

Ribonucleotide

Type description

DNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

G

Defined at

2016-05-13

Last modified at

2016-05-27

Status

Released

Obsoleted

Not Assigned



8AA : Atoms of Molecule

Total Number of Atoms: 65
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 6.403 -2.901 0.437
2 N1 N N1 N N N 0 3.271 4.278 -0.952
3 C2 C C2 N N N 0 3.707 3.088 -1.306
4 N2 N N2 N N N 0 4.872 2.999 -2.02
5 C3 C C3 N Y N 0 -7.61 -2.044 0.882
6 N3 N N3 N N N 0 3.045 1.945 -0.99
7 C4 C C4 N Y N 0 1.875 1.991 -0.276
8 N4 N N4 N N N 0 -1.093 1.117 1.461
9 C5 C C5 N Y N 0 1.378 3.227 0.118
10 C6 C C6 N N N 0 2.136 4.425 -0.251
11 O6 O O6 N N N 0 1.742 5.536 0.071
12 C7 C C7 N Y N 0 -8.692 -2.319 0.109
13 N7 N N7 N Y N 0 0.228 3.005 0.8
14 C8 C C8 N Y N 0 -0.002 1.717 0.844
15 C9 C C9 N N N 0 -1.053 0.839 2.779
16 N9 N N9 N Y N 0 0.998 1.055 0.186
17 C1' C C1' R N N 0 1.106 -0.396 0.011
18 C10 C C10 N N N 0 0.134 1.265 3.603
19 C11 C C11 N Y N 0 -8.779 -1.883 -1.213
20 O11 O O11 N N N 0 -1.973 0.246 3.302
21 C12 C C12 N Y N 0 -2.234 0.801 0.713
22 C13 C C13 N Y N 0 -2.326 1.242 -0.614
23 C14 C C14 N Y N 0 -3.408 0.964 -1.383
24 C15 C C15 N Y N 0 -4.475 0.213 -0.843
25 C16 C C16 N Y N 0 -4.381 -0.25 0.546
26 C17 C C17 N Y N 0 -3.229 0.072 1.293
27 C18 C C18 N Y N 0 -5.597 -0.092 -1.609
28 C19 C C19 N Y N 0 -6.636 -0.831 -1.045
29 C2' C C2' N N N 0 0.748 -0.777 -1.438
30 C20 C C20 N Y N 0 -6.543 -1.294 0.344
31 C21 C C21 N Y N 0 -5.418 -0.993 1.109
32 C22 C C22 N Y N 0 -7.785 -1.163 -1.793
33 C3' C C3' S N N 0 2.016 -1.492 -1.966
34 C5' C C5' N N N 0 4.222 -2.092 -0.878
35 O3' O O3' N N N 0 1.666 -2.633 -2.753
36 C4' C C4' R N N 0 2.718 -1.92 -0.653
37 O4' O O4' N N N 0 2.461 -0.816 0.245
38 O5' O O5' N N N 0 4.827 -2.598 0.314
39 OP1 O OP1 N N N 0 6.595 -3.037 2.03
40 OP2 O OP2 N N N 0 6.488 -4.435 -0.044
41 HN2 H HN2 N N N 0 5.359 3.804 -2.255
42 HN2A H HN2A N N N 0 5.21 2.131 -2.291
43 H3 H H3 N N N 0 -7.569 -2.393 1.904
44 HN3 H HN3 N N N 0 3.402 1.088 -1.272
45 H7 H H7 N N N 0 -9.507 -2.89 0.529
46 H1' H H1' N N N 0 0.436 -0.904 0.705
47 H10 H H10 N N N 0 0.892 1.7 2.951
48 H10A H H10A N N N 0 -0.181 2.006 4.338
49 H10B H H10B N N N 0 0.551 0.398 4.116
50 H11 H H11 N N N 0 -9.659 -2.126 -1.79
51 H13 H H13 N N N 0 -1.515 1.817 -1.035
52 H14 H H14 N N N 0 -3.453 1.316 -2.403
53 H17 H H17 N N N 0 -3.136 -0.257 2.318
54 H18 H H18 N N N 0 -5.664 0.245 -2.633
55 H22 H H22 N N N 0 -7.879 -0.835 -2.818
56 H2' H H2' N N N 0 -0.106 -1.453 -1.455
57 H2'A H H2'A N N N 0 0.539 0.116 -2.027
58 H21 H H21 N N N 0 -5.349 -1.334 2.132
59 H3' H H3' N N N 0 2.641 -0.805 -2.536
60 HO3' H HO3' N N N 0 1.146 -2.424 -3.54
61 H4' H H4' N N N 0 2.279 -2.838 -0.264
62 H5' H H5' N N N 0 4.389 -2.794 -1.695
63 H5'A H H5'A N N N 0 4.665 -1.129 -1.13
64 HOP1 H HOP1 N N N 0 7.504 -3.225 2.302
65 HOP2 H HOP2 N N N 0 7.383 -4.801 -0.036



8AA : Chemical Bonds

Total Number of Bonds: 70
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OP2 P O P sing 1.61 N N
2 OP1 P O P sing 1.61 N N
3 P O5' P O sing 1.61 N N
4 C2 N1 C N doub 1.32 N N
5 N1 C6 N C sing 1.34 N N
6 N2 C2 N C sing 1.37 N N
7 C2 N3 C N sing 1.36 N N
8 N2 HN2 N H sing 0.97 N N
9 N2 HN2A N H sing 0.97 N N
10 C20 C3 C C doub 1.41 N Y
11 C3 C7 C C sing 1.36 N Y
12 C3 H3 C H sing 1.08 N N
13 N3 C4 N C sing 1.37 N N
14 N3 HN3 N H sing 0.97 N N
15 C4 N9 C N sing 1.36 N Y
16 C4 C5 C C doub 1.39 N Y
17 C8 N4 C N sing 1.39 N N
18 C9 N4 C N sing 1.35 N N
19 N4 C12 N C sing 1.4 N N
20 C6 C5 C C sing 1.46 N N
21 C5 N7 C N sing 1.36 N Y
22 C6 O6 C O doub 1.22 N N
23 C7 C11 C C doub 1.39 N Y
24 C7 H7 C H sing 1.08 N N
25 C8 N7 C N doub 1.31 N Y
26 N9 C8 N C sing 1.37 N Y
27 O11 C9 O C doub 1.21 N N
28 C9 C10 C C sing 1.51 N N
29 C1' N9 C N sing 1.47 N N
30 C2' C1' C C sing 1.54 N N
31 O4' C1' O C sing 1.44 N N
32 C1' H1' C H sing 1.09 N N
33 C10 H10 C H sing 1.09 N N
34 C10 H10A C H sing 1.09 N N
35 C10 H10B C H sing 1.09 N N
36 C22 C11 C C sing 1.36 N Y
37 C11 H11 C H sing 1.08 N N
38 C12 C13 C C sing 1.4 N Y
39 C12 C17 C C doub 1.36 N Y
40 C13 C14 C C doub 1.36 N Y
41 C13 H13 C H sing 1.08 N N
42 C14 C15 C C sing 1.41 N Y
43 C14 H14 C H sing 1.08 N N
44 C16 C15 C C sing 1.47 N Y
45 C15 C18 C C doub 1.39 N Y
46 C17 C16 C C sing 1.41 N Y
47 C16 C21 C C doub 1.39 N Y
48 C17 H17 C H sing 1.08 N N
49 C18 C19 C C sing 1.39 N Y
50 C18 H18 C H sing 1.08 N N
51 C20 C19 C C sing 1.47 N Y
52 C19 C22 C C doub 1.41 N Y
53 C3' C2' C C sing 1.55 N N
54 C2' H2' C H sing 1.09 N N
55 C2' H2'A C H sing 1.09 N N
56 C21 C20 C C sing 1.39 N Y
57 C21 H21 C H sing 1.08 N N
58 C22 H22 C H sing 1.08 N N
59 O3' C3' O C sing 1.43 N N
60 C3' C4' C C sing 1.55 N N
61 C3' H3' C H sing 1.09 N N
62 O3' HO3' O H sing 0.97 N N
63 C5' C4' C C sing 1.53 N N
64 C4' O4' C O sing 1.45 N N
65 C4' H4' C H sing 1.09 N N
66 C5' O5' C O sing 1.43 N N
67 C5' H5' C H sing 1.09 N N
68 C5' H5'A C H sing 1.09 N N
69 OP1 HOP1 O H sing 0.97 N N
70 OP2 HOP2 O H sing 0.97 N N



8AA : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
8AA 5g34 Open in New Window Polymer component 2 1