Chemical Components in the PDB

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AP7 : Summary

Code

AP7

One-letter code

A

Molecule name

N1-PROTONATED ADENOSINE-5'-MONOPHOSPHATE

Systematic names

ProgramVersionName
ACDLabs 12.01 5'-adenylic acid
OpenEye OEToolkits 1.7.0 [(2R,3S,4R,5R)-5-(6-azanylpurin-1-ium-9-yl)-3,4-dihydroxy-oxolan-2-yl]methyl dihydrogen phosphate

Formula

C10 H15 N5 O7 P

Formal charge

1

Molecular weight

348.229 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC3OC(n2cnc1c(N)[nH+]cnc12)C(O)C3O
SMILES CACTVS 3.370 Nc1[nH+]cnc2n(cnc12)[CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.7.0 c1[nH+]c(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O)O)O)N
Canonical SMILES CACTVS 3.370 Nc1[nH+]cnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.7.0 c1[nH+]c(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O)O)O)N

IUPAC InChI

InChI=1S/C10H14N5O7P/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(22-10)1-21-23(18,19)20/h2-4,6-7,10,16-17H,1H2,(H2,11,12,13)(H2,18,19,20)/p+1/t4-,6-,7-,10-/m1/s1

IUPAC InChI key

UDMBCSSLTHHNCD-KQYNXXCUSA-O
AP7

wwPDB Information

Atom count

38 (23 without Hydrogen)

Polymer type

Ribonucleotide

Type description

RNA LINKING

Type code

ATOMN

Is modified

Yes

Standard parent

A

Defined at

2004-08-10

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



AP7 : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1' R N N 0 -0.717 0.818 -0.421
2 N1 N N1 N Y N 1 -5.765 -0.407 -0.38
3 C2 C C2 N Y N 0 -5.19 0.712 -0.782
4 N3 N N3 N Y N 0 -3.887 0.893 -0.738
5 C4 C C4 N Y N 0 -3.086 -0.063 -0.277
6 C5 C C5 N Y N 0 -3.649 -1.272 0.163
7 C6 C C6 N Y N 0 -5.045 -1.418 0.095
8 N6 N N6 N N N 0 -5.656 -2.586 0.515
9 N7 N N7 N Y N 0 -2.628 -2.061 0.575
10 C8 C C8 N Y N 0 -1.501 -1.428 0.42
11 N9 N N9 N Y N 0 -1.731 -0.191 -0.103
12 C2' C C2' R N N 0 -0.55 1.814 0.754
13 O2' O O2' N N N 0 -1.497 2.879 0.659
14 C3' C C3' S N N 0 0.891 2.335 0.536
15 O3' O O3' N N N 0 0.871 3.588 -0.151
16 C4' C C4' R N N 0 1.556 1.253 -0.336
17 O4' O O4' N N N 0 0.587 0.209 -0.535
18 C5' C C5' N N N 0 2.786 0.691 0.379
19 O5' O O5' N N N 0 3.462 -0.226 -0.484
20 OP1 O O1P N N N 0 4.562 -1.745 1.206
21 OP2 O O2P N N N 0 5.21 -2.049 -1.215
22 P P P N N N 0 4.802 -1.008 -0.056
23 OP3 O O3P N N Y 0 5.996 0.051 0.16
24 H1' H H1' N N N 0 -0.978 1.347 -1.338
25 H1 H H1 N N N 0 -6.73 -0.491 -0.43
26 H2 H H2 N N N 0 -5.812 1.509 -1.162
27 H61 H H61 N N N 0 -6.621 -2.674 0.463
28 H62 H H62 N N N 0 -5.12 -3.317 0.86
29 H8 H H8 N N N 0 -0.528 -1.825 0.669
30 H2' H H2' N N N 0 -0.638 1.303 1.713
31 HO2' H HO'2 N N N 0 -1.433 3.529 1.372
32 H3' H H3' N N N 0 1.411 2.432 1.489
33 HO3' H H3T N N Y 0 0.413 4.292 0.328
34 H4' H H4' N N N 0 1.845 1.677 -1.298
35 H5'' H H5'2 N N N 0 3.46 1.508 0.639
36 H5' H H5'1 N N N 0 2.475 0.174 1.286
37 HOP2 H HOP2 N N N 0 6.011 -2.556 -1.024
38 HOP3 H HOP3 N N N 0 6.208 0.57 -0.628



AP7 : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1' N9 C N sing 1.47 N N
2 C1' C2' C C sing 1.55 N N
3 C1' O4' C O sing 1.44 N N
4 C1' H1' C H sing 1.09 N N
5 N1 C2 N C sing 1.32 N Y
6 N1 C6 N C doub 1.33 N Y
7 N1 H1 N H sing 0.97 N N
8 C2 N3 C N doub 1.32 N Y
9 C2 H2 C H sing 1.08 N N
10 N3 C4 N C sing 1.33 N Y
11 C4 C5 C C doub 1.4 N Y
12 C4 N9 C N sing 1.37 N Y
13 C5 C6 C C sing 1.41 N Y
14 C5 N7 C N sing 1.35 N Y
15 C6 N6 C N sing 1.38 N N
16 N6 H61 N H sing 0.97 N N
17 N6 H62 N H sing 0.97 N N
18 N7 C8 N C doub 1.3 N Y
19 C8 N9 C N sing 1.36 N Y
20 C8 H8 C H sing 1.08 N N
21 C2' O2' C O sing 1.43 N N
22 C2' C3' C C sing 1.55 N N
23 C2' H2' C H sing 1.09 N N
24 O2' HO2' O H sing 0.97 N N
25 C3' O3' C O sing 1.43 N N
26 C3' C4' C C sing 1.54 N N
27 C3' H3' C H sing 1.09 N N
28 O3' HO3' O H sing 0.97 N N
29 C4' O4' C O sing 1.44 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'' C H sing 1.09 N N
34 C5' H5' C H sing 1.09 N N
35 O5' P O P sing 1.61 N N
36 OP1 P O P doub 1.48 N N
37 OP2 P O P sing 1.61 N N
38 OP2 HOP2 O H sing 0.97 N N
39 P OP3 P O sing 1.61 N N
40 OP3 HOP3 O H sing 0.97 N N



AP7 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
AP7 1u6p Open in New Window Polymer component 1 1
AP7 2rrc Open in New Window Polymer component 1 1
AP7 5lwj Open in New Window Polymer component 1 1