Chemical Components in the PDB

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F3N : Summary

Code

F3N

One-letter code

A

Molecule name

3'-deoxy-3'-(L-phenylalanylamino)adenosine 5'-(dihydrogen phosphate)

Systematic names

ProgramVersionName
ACDLabs 12.01 3'-deoxy-3'-(L-phenylalanylamino)adenosine 5'-(dihydrogen phosphate)
OpenEye OEToolkits 1.7.6 [(2S,3S,4R,5R)-5-(6-aminopurin-9-yl)-3-[[(2S)-2-azanyl-3-phenyl-propanoyl]amino]-4-oxidanyl-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C19 H24 N7 O7 P

Formal charge

0

Molecular weight

493.41 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC4OC(n2cnc1c(ncnc12)N)C(O)C4NC(=O)C(N)Cc3ccccc3
SMILES CACTVS 3.385 N[CH](Cc1ccccc1)C(=O)N[CH]2[CH](O)[CH](O[CH]2CO[P](O)(O)=O)n3cnc4c(N)ncnc34
SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)CC(C(=O)NC2C(OC(C2O)n3cnc4c3ncnc4N)COP(=O)(O)O)N
Canonical SMILES CACTVS 3.385 N[C@@H](Cc1ccccc1)C(=O)N[C@H]2[C@@H](O)[C@@H](O[C@@H]2CO[P](O)(O)=O)n3cnc4c(N)ncnc34
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)C[C@@H](C(=O)N[C@@H]2[C@H](O[C@H]([C@@H]2O)n3cnc4c3ncnc4N)COP(=O)(O)O)N

IUPAC InChI

InChI=1S/C19H24N7O7P/c20-11(6-10-4-2-1-3-5-10)18(28)25-13-12(7-32-34(29,30)31)33-19(15(13)27)26-9-24-14-16(21)22-8-23-17(14)26/h1-5,8-9,11-13,15,19,27H,6-7,20H2,(H,25,28)(H2,21,22,23)(H2,29,30,31)/t11-,12+,13+,15+,19+/m0/s1

IUPAC InChI key

FGNMGARNYLAFLT-YCOMJZELSA-N
F3N

wwPDB Information

Atom count

58 (34 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

A

Defined at

2014-05-18

Last modified at

2014-08-15

Status

Released

Obsoleted

Not Assigned



F3N : Atoms of Molecule

Total Number of Atoms: 58
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 0.054 5.181 0.164
2 OP1 O OP1 N N N 0 1.48 5.345 -0.197
3 OP2 O OP2 N N N 0 -0.869 5.635 -1.075
4 C1' C C1' R N N 0 -2.047 -0.282 0.468
5 C2' C C2' R N N 0 -1.059 -0.965 -0.504
6 O2' O O2' N N N 0 -0.575 -2.189 0.053
7 C3' C C3' S N N 0 0.091 0.056 -0.65
8 N3' N N3' N N N 0 1.352 -0.521 -0.175
9 C4' C C4' S N N 0 -0.337 1.235 0.251
10 O4' O O4' N N N 0 -1.775 1.13 0.337
11 C5' C C5' N N N 0 0.063 2.566 -0.388
12 O5' O O5' N N N 0 -0.237 3.636 0.511
13 C6 C C6 N Y N 0 -6.403 -2.492 0.104
14 N9 N N9 N Y N 0 -3.429 -0.574 0.079
15 C8 C C8 N Y N 0 -4.209 0.176 -0.751
16 N7 N N7 N Y N 0 -5.381 -0.376 -0.877
17 N6 N N6 N N N 0 -7.655 -2.406 -0.48
18 C5 C C5 N Y N 0 -5.427 -1.511 -0.139
19 N3 N N3 N Y N 0 -3.957 -2.705 1.263
20 C4 C C4 N Y N 0 -4.174 -1.654 0.479
21 C2 C C2 N Y N 0 -4.899 -3.603 1.458
22 N1 N N1 N Y N 0 -6.091 -3.513 0.896
23 C C C N N N 0 2.118 -1.248 -1.013
24 O O O N N N 0 1.763 -1.425 -2.159
25 CA C CA S N N 0 3.414 -1.841 -0.525
26 N N N N N N 0 3.814 -2.942 -1.412
27 CB C CB N N N 0 4.501 -0.763 -0.529
28 CG C CG N Y N 0 5.764 -1.322 0.073
29 CD1 C CD1 N Y N 0 5.985 -1.22 1.434
30 CE1 C CE1 N Y N 0 7.142 -1.737 1.987
31 CZ C CZ N Y N 0 8.077 -2.356 1.179
32 CE2 C CE2 N Y N 0 7.856 -2.459 -0.181
33 CD2 C CD2 N Y N 0 6.7 -1.941 -0.735
34 OP3 O OP3 N N Y 0 -0.284 6.092 1.447
35 HOP2 H HOP2 N N N 0 -1.818 5.554 -0.909
36 H1' H H1' N N N 0 -1.864 -0.61 1.491
37 H2' H H2' N N N 0 -1.536 -1.148 -1.467
38 HO2' H HO2' N N N 0 -1.266 -2.845 0.222
39 H3' H H3' N N N 0 0.184 0.38 -1.686
40 H6 H H6 N N N 0 1.636 -0.379 0.741
41 H4' H H4' N N N 0 0.11 1.139 1.241
42 H5' H H5' N N N 0 1.131 2.56 -0.602
43 H5'' H H5'' N N N 0 -0.493 2.705 -1.316
44 H8 H H8 N N N 0 -3.9 1.092 -1.232
45 H61 H H61 N N N 0 -8.317 -3.095 -0.313
46 H62 H H62 N N N 0 -7.871 -1.656 -1.056
47 HA H HA N N N 0 3.282 -2.22 0.488
48 H H H N N N 0 3.143 -3.695 -1.377
49 H2 H H2 N N N 0 -4.69 -4.445 2.101
50 HB3 H HB3 N N N 0 4.696 -0.447 -1.554
51 HB2 H HB2 N N N 0 4.166 0.092 0.058
52 HD1 H HD1 N N N 0 5.254 -0.737 2.065
53 HE1 H HE1 N N N 0 7.315 -1.658 3.05
54 HZ H HZ N N N 0 8.981 -2.76 1.611
55 HE2 H HE2 N N N 0 8.587 -2.942 -0.812
56 HD2 H HD2 N N N 0 6.525 -2.024 -1.797
57 HOP3 H HOP3 N N N 0 -0.132 7.037 1.31
58 H1 H H1 N N N 0 3.943 -2.615 -2.358



F3N : Chemical Bonds

Total Number of Bonds: 61
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CE1 CZ C C doub 1.38 N Y
2 CE1 CD1 C C sing 1.38 N Y
3 N CA N C sing 1.47 N N
4 CZ CE2 C C sing 1.38 N Y
5 CD1 CG C C doub 1.38 N Y
6 CE2 CD2 C C doub 1.38 N Y
7 CG CD2 C C sing 1.38 N Y
8 CG CB C C sing 1.51 N N
9 CA CB C C sing 1.53 N N
10 CA C C C sing 1.51 N N
11 O C O C doub 1.21 N N
12 C N3' C N sing 1.35 N N
13 N3' C3' N C sing 1.47 N N
14 C3' C2' C C sing 1.54 N N
15 C3' C4' C C sing 1.54 N N
16 O5' C5' O C sing 1.43 N N
17 O5' P O P sing 1.61 N N
18 C5' C4' C C sing 1.53 N N
19 OP1 P O P doub 1.48 N N
20 C2' O2' C O sing 1.43 N N
21 C2' C1' C C sing 1.55 N N
22 C4' O4' C O sing 1.44 N N
23 OP2 P O P sing 1.61 N N
24 C8 N7 C N doub 1.3 N Y
25 C8 N9 C N sing 1.36 N Y
26 C1' O4' C O sing 1.44 N N
27 C1' N9 C N sing 1.47 N N
28 N7 C5 N C sing 1.35 N Y
29 N9 C4 N C sing 1.37 N Y
30 C5 C4 C C doub 1.4 N Y
31 C5 C6 C C sing 1.4 N Y
32 C4 N3 C N sing 1.33 N Y
33 N6 C6 N C sing 1.38 N N
34 C6 N1 C N doub 1.33 N Y
35 N3 C2 N C doub 1.32 N Y
36 N1 C2 N C sing 1.32 N Y
37 P OP3 P O sing 1.61 N N
38 OP2 HOP2 O H sing 0.97 N N
39 C1' H1' C H sing 1.09 N N
40 C2' H2' C H sing 1.09 N N
41 O2' HO2' O H sing 0.97 N N
42 C3' H3' C H sing 1.09 N N
43 N3' H6 N H sing 0.97 N N
44 C4' H4' C H sing 1.09 N N
45 C5' H5' C H sing 1.09 N N
46 C5' H5'' C H sing 1.09 N N
47 C8 H8 C H sing 1.08 N N
48 N6 H61 N H sing 0.97 N N
49 N6 H62 N H sing 0.97 N N
50 C2 H2 C H sing 1.08 N N
51 CA HA C H sing 1.09 N N
52 N H N H sing 1.01 N N
53 CB HB3 C H sing 1.09 N N
54 CB HB2 C H sing 1.09 N N
55 CD1 HD1 C H sing 1.08 N N
56 CE1 HE1 C H sing 1.08 N N
57 CZ HZ C H sing 1.08 N N
58 CE2 HE2 C H sing 1.08 N N
59 CD2 HD2 C H sing 1.08 N N
60 OP3 HOP3 O H sing 0.97 N N
61 N H1 N H sing 1.01 N N



F3N : Used in PDB Entries

Total Number of PDB Entries: 14
Ligand Code PDB Entry ID Type Total Distinct
F3N 1vy4 Open in New Window Polymer component 2 1
F3N 4wpo Open in New Window Polymer component 2 1
F3N 5wit Open in New Window Polymer component 2 1
F3N 6xhv Open in New Window Polymer component 2 1
F3N 6xhw Open in New Window Polymer component 2 1
F3N 6xhy Open in New Window Polymer component 2 1
F3N 7rq8 Open in New Window Polymer component 2 1
F3N 7rq9 Open in New Window Polymer component 2 1
F3N 8cvj Open in New Window Polymer component 2 1
F3N 8cvk Open in New Window Polymer component 2 1
F3N 8cvl Open in New Window Polymer component 2 1
F3N 8g29 Open in New Window Polymer component 2 1
F3N 8g2a Open in New Window Polymer component 2 1
F3N 8g2c Open in New Window Polymer component 2 1