Chemical Components in the PDB

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MFO : Summary

Code

MFO

One-letter code

G

Molecule name

[(2~{R},3~{S},5~{R})-5-[2-azanyl-8-[ethanoyl(naphthalen-2-yl)amino]-6-oxidanylidene-3~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.5 [(2~{R},3~{S},5~{R})-5-[2-azanyl-8-[ethanoyl(naphthalen-2-yl)amino]-6-oxidanylidene-3~{H}-purin-9-yl]-3-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C22 H23 N6 O8 P

Formal charge

0

Molecular weight

530.427 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC(=O)N(c1ccc2ccccc2c1)c3nc4C(=O)N=C(N)Nc4n3[CH]5C[CH](O)[CH](CO[P](O)(O)=O)O5
SMILES OpenEye OEToolkits 2.0.5 CC(=O)N(c1ccc2ccccc2c1)c3nc4c(n3C5CC(C(O5)COP(=O)(O)O)O)NC(=NC4=O)N
Canonical SMILES CACTVS 3.385 CC(=O)N(c1ccc2ccccc2c1)c3nc4C(=O)N=C(N)Nc4n3[C@H]5C[C@H](O)[C@@H](CO[P](O)(O)=O)O5
Canonical SMILES OpenEye OEToolkits 2.0.5 CC(=O)N(c1ccc2ccccc2c1)c3nc4c(n3[C@H]5C[C@@H]([C@H](O5)COP(=O)(O)O)O)NC(=NC4=O)N

IUPAC InChI

InChI=1S/C22H23N6O8P/c1-11(29)27(14-7-6-12-4-2-3-5-13(12)8-14)22-24-18-19(25-21(23)26-20(18)31)28(22)17-9-15(30)16(36-17)10-35-37(32,33)34/h2-8,15-17,30H,9-10H2,1H3,(H2,32,33,34)(H3,23,25,26,31)/t15-,16+,17+/m0/s1

IUPAC InChI key

AEEKNUIQRYLODW-GVDBMIGSSA-N
MFO

wwPDB Information

Atom count

60 (37 without Hydrogen)

Polymer type

Deoxy ribonucleotide

Type description

DNA linking

Type code

ATOMN

Is modified

Yes

Standard parent

DG

Defined at

2016-04-06

Last modified at

2019-05-07

Status

Released

Obsoleted

Not Assigned



MFO : Atoms of Molecule

Total Number of Atoms: 60
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C6 C C1 N N N 0 0.394 -4.217 -0.064
2 C5 C C2 N Y N 0 0.655 -2.812 0.259
3 C4 C C3 N Y N 0 -0.253 -1.858 -0.182
4 C8 C C4 N Y N 0 1.379 -0.877 0.926
5 N4 N N1 N N N 0 2.167 0.102 1.52
6 C2 C C5 N N N 0 -1.543 -3.585 -1.168
7 C21 C C6 N Y N 0 6.541 -0.276 -0.538
8 C10 C C7 N N N 0 0.834 -0.184 3.584
9 C9 C C8 N N N 0 1.905 0.505 2.779
10 C12 C C9 N Y N 0 3.232 0.67 0.81
11 C20 C C10 N Y N 0 7.557 0.31 -1.228
12 N3 N N2 N N N 0 -1.349 -2.268 -0.896
13 C15 C C11 N Y N 0 5.325 1.835 -0.6
14 C14 C C12 N Y N 0 4.185 2.589 -0.272
15 C13 C C13 N Y N 0 3.166 2.012 0.418
16 N1 N N3 N N N 0 -0.707 -4.52 -0.768
17 C19 C C14 N Y N 0 7.483 1.647 -1.614
18 C18 C C15 N Y N 0 6.394 2.405 -1.312
19 N2 N N4 N N N 0 -2.651 -3.954 -1.884
20 C17 C C16 N Y N 0 4.331 -0.1 0.499
21 C16 C C17 N Y N 0 5.4 0.475 -0.207
22 P P P1 N N N 0 -6.232 1.201 0.267
23 C4' C C19 R N N 0 -2.382 1.692 -0.548
24 OP1 O O1 N N Y 0 -6.87 2.197 -0.623
25 O5' O O2 N N N 0 -4.639 1.432 0.276
26 C5' C C18 N N N 0 -3.848 1.451 -0.914
27 C3' C C20 S N N 0 -1.521 1.803 -1.826
28 O3' O O3 N N N 0 -1.287 3.174 -2.155
29 C2' C C21 N N N 0 -0.196 1.104 -1.448
30 C1' C C22 R N N 0 -0.414 0.653 0.014
31 O4' O O4 N N N 0 -1.848 0.553 0.162
32 N9 N N5 N Y N 0 0.215 -0.65 0.245
33 N7 N N6 N Y N 0 1.636 -2.16 0.932
34 O6 O O5 N N N 0 1.164 -5.093 0.296
35 OP2 O O6 N N Y 0 -6.808 1.371 1.761
36 O11 O O7 N N N 0 2.532 1.423 3.264
37 O1 O O8 N N Y 0 -6.556 -0.282 -0.268
38 H1 H H1 N N N 0 6.61 -1.315 -0.249
39 H2 H H2 N N N 0 0.321 -0.914 2.957
40 H3 H H3 N N N 0 1.288 -0.691 4.435
41 H4 H H4 N N N 0 0.116 0.554 3.941
42 H5 H H5 N N N 0 8.433 -0.269 -1.48
43 H6 H H6 N N N 0 -1.992 -1.613 -1.21
44 H7 H H7 N N N 0 4.119 3.626 -0.567
45 H8 H H8 N N N 0 2.293 2.597 0.667
46 H9 H H9 N N N 0 8.303 2.089 -2.161
47 H10 H H10 N N N 0 6.351 3.44 -1.618
48 H11 H H11 N N N 0 -3.279 -3.28 -2.187
49 H12 H H12 N N N 0 -2.807 -4.89 -2.088
50 H13 H H13 N N N 0 4.375 -1.135 0.805
51 H14 H H14 N N N 0 -3.942 0.495 -1.428
52 H15 H H15 N N N 0 -4.196 2.251 -1.568
53 H16 H H16 N N N 0 -2.285 2.595 0.054
54 H17 H H17 N N N 0 -2.003 1.288 -2.657
55 H18 H H18 N N N 0 -0.751 3.302 -2.949
56 H19 H H19 N N N 0 -0.022 0.242 -2.091
57 H20 H H20 N N N 0 0.637 1.803 -1.514
58 H21 H H21 N N N 0 -0.013 1.396 0.704
59 H22 H H22 N N N 0 -7.764 1.245 1.831
60 H23 H H23 N N N 0 -6.169 -0.988 0.269



MFO : Chemical Bonds

Total Number of Bonds: 64
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C19 C18 C C doub 1.36 N Y
2 C19 C20 C C sing 1.39 N Y
3 C18 C15 C C sing 1.41 N Y
4 C20 C21 C C doub 1.36 N Y
5 C15 C14 C C doub 1.41 N Y
6 C15 C16 C C sing 1.42 N Y
7 C14 C13 C C sing 1.36 N Y
8 C21 C16 C C sing 1.41 N Y
9 C16 C17 C C doub 1.4 N Y
10 C13 C12 C C doub 1.4 N Y
11 C17 C12 C C sing 1.38 N Y
12 C12 N4 C N sing 1.4 N N
13 N4 C9 N C sing 1.35 N N
14 N4 C8 N C sing 1.39 N N
15 C10 C9 C C sing 1.51 N N
16 C9 O11 C O doub 1.21 N N
17 N7 C8 N C doub 1.31 N Y
18 N7 C5 N C sing 1.36 N Y
19 C8 N9 C N sing 1.37 N Y
20 O6 C6 O C doub 1.22 N N
21 C5 C6 C C sing 1.47 N N
22 C5 C4 C C doub 1.39 N Y
23 N9 C1' N C sing 1.47 N N
24 N9 C4 N C sing 1.36 N Y
25 C6 N1 C N sing 1.34 N N
26 C1' C2' C C sing 1.55 N N
27 C1' O4' C O sing 1.45 N N
28 C4 N3 C N sing 1.37 N N
29 C2' C3' C C sing 1.55 N N
30 O4' C4' O C sing 1.44 N N
31 N1 C2 N C doub 1.32 N N
32 N3 C2 N C sing 1.36 N N
33 C3' C4' C C sing 1.54 N N
34 C3' O3' C O sing 1.43 N N
35 C2 N2 C N sing 1.37 N N
36 C4' C5' C C sing 1.53 N N
37 O5' C5' O C sing 1.43 N N
38 O5' P O P sing 1.61 N N
39 P OP1 P O doub 1.48 N N
40 P OP2 P O sing 1.61 N N
41 P O1 P O sing 1.61 N N
42 C21 H1 C H sing 1.08 N N
43 C10 H2 C H sing 1.09 N N
44 C10 H3 C H sing 1.09 N N
45 C10 H4 C H sing 1.09 N N
46 C20 H5 C H sing 1.08 N N
47 N3 H6 N H sing 0.97 N N
48 C14 H7 C H sing 1.08 N N
49 C13 H8 C H sing 1.08 N N
50 C19 H9 C H sing 1.08 N N
51 C18 H10 C H sing 1.08 N N
52 N2 H11 N H sing 0.97 N N
53 N2 H12 N H sing 0.97 N N
54 C17 H13 C H sing 1.08 N N
55 C5' H14 C H sing 1.09 N N
56 C5' H15 C H sing 1.09 N N
57 C4' H16 C H sing 1.09 N N
58 C3' H17 C H sing 1.09 N N
59 O3' H18 O H sing 0.97 N N
60 C2' H19 C H sing 1.09 N N
61 C2' H20 C H sing 1.09 N N
62 C1' H21 C H sing 1.09 N N
63 OP2 H22 O H sing 0.97 N N
64 O1 H23 O H sing 0.97 N N



MFO : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
MFO 5g33 Open in New Window Polymer component 2 1