Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

3AM : Summary

Code

3AM

One-letter code

X

Molecule name

[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate

Synonyms

3'-AMP

Systematic names

ProgramVersionName
ACDLabs 10.04 3'-adenylic acid
OpenEye OEToolkits 1.5.0 [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl] dihydrogen phosphate

Formula

C10 H14 N5 O7 P

Formal charge

0

Molecular weight

347.221 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=P(O)(O)OC3C(OC(n2cnc1c(ncnc12)N)C3O)CO
SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[CH]3O[CH](CO)[CH](O[P](O)(O)=O)[CH]3O
SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CO)OP(=O)(O)O)O)N
Canonical SMILES CACTVS 3.341 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO)[C@@H](O[P](O)(O)=O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.5.0 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO)OP(=O)(O)O)O)N

IUPAC InChI

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

IUPAC InChI key

LNQVTSROQXJCDD-KQYNXXCUSA-N
3AM

wwPDB Information

Atom count

37 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-01-23

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



3AM : Atoms of Molecule

Total Number of Atoms: 37
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O1P O O1P N N N 0 -4.939 0.097 -0.475
2 P P P N N N 0 -3.993 1.169 -0.091
3 O2P O O2P N N N 0 -3.684 2.096 -1.371
4 O3P O O3P N N N 0 -4.644 2.067 1.077
5 O2' O O2* N N N 0 -0.398 1.544 -0.429
6 C2' C C2* R N N 0 -0.436 0.125 -0.589
7 C3' C C3* S N N 0 -1.86 -0.423 -0.328
8 O3' O O3* N N N 0 -2.623 0.512 0.439
9 C1' C C1* R N N 0 0.39 -0.578 0.518
10 O4' O O4* N N N 0 -0.205 -1.891 0.6
11 C4' C C4* R N N 0 -1.627 -1.716 0.476
12 C5' C C5* N N N 0 -2.234 -2.908 -0.267
13 O5' O O5* N N N 0 -2.116 -4.082 0.538
14 N9 N N9 N Y N 0 1.799 -0.674 0.129
15 C8 C C8 N Y N 0 2.399 -1.74 -0.473
16 N7 N N7 N Y N 0 3.659 -1.484 -0.676
17 C5 C C5 N Y N 0 3.947 -0.242 -0.219
18 C6 C C6 N Y N 0 5.107 0.548 -0.169
19 N6 N N6 N N N 0 6.308 0.075 -0.669
20 C4 C C4 N Y N 0 2.755 0.295 0.298
21 N3 N N3 N Y N 0 2.768 1.522 0.809
22 C2 C C2 N Y N 0 3.879 2.228 0.829
23 N1 N N1 N Y N 0 5.025 1.761 0.367
24 HO2P H HO2P N N N 0 -3.07 2.821 -1.192
25 HO3P H HO3P N N N 0 -5.475 2.495 0.827
26 HO2' H HO2* N N N 0 0.474 1.934 -0.582
27 H2' H H2* N N N 0 -0.084 -0.163 -1.579
28 H3' H H3* N N N 0 -2.363 -0.642 -1.27
29 H1' H H1* N N N 0 0.288 -0.051 1.467
30 H4' H H4* N N N 0 -2.076 -1.625 1.465
31 H5' H H5* N N N 0 -3.287 -2.711 -0.47
32 H5'A H H5*A N N N 0 -1.705 -3.057 -1.208
33 HO5' H HO5* N N N 0 -2.482 -4.878 0.129
34 H8 H H8 N N N 0 1.902 -2.66 -0.742
35 HN6 H HN6 N N N 0 6.355 -0.812 -1.058
36 HN6A H HN6A N N N 0 7.102 0.63 -0.629
37 H2 H H2 N N N 0 3.855 3.222 1.251



3AM : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1P P O P doub 1.48 N N
2 P O2P P O sing 1.61 N N
3 P O3P P O sing 1.61 N N
4 P O3' P O sing 1.61 N N
5 O2' C2' O C sing 1.43 N N
6 C2' C3' C C sing 1.55 N N
7 C2' C1' C C sing 1.55 N N
8 C3' O3' C O sing 1.43 N N
9 C3' C4' C C sing 1.54 N N
10 C1' O4' C O sing 1.44 N N
11 C1' N9 C N sing 1.46 N N
12 O4' C4' O C sing 1.44 N N
13 C4' C5' C C sing 1.53 N N
14 C5' O5' C O sing 1.43 N N
15 N9 C8 N C sing 1.36 N Y
16 N9 C4 N C sing 1.37 N Y
17 C8 N7 C N doub 1.3 N Y
18 N7 C5 N C sing 1.35 N Y
19 C5 C6 C C doub 1.4 N Y
20 C5 C4 C C sing 1.41 N Y
21 C6 N6 C N sing 1.38 N N
22 C6 N1 C N sing 1.33 N Y
23 C4 N3 C N doub 1.33 N Y
24 N3 C2 N C sing 1.32 N Y
25 C2 N1 C N doub 1.32 N Y
26 O2P HO2P O H sing 0.97 N N
27 O3P HO3P O H sing 0.97 N N
28 O2' HO2' O H sing 0.97 N N
29 C2' H2' C H sing 1.09 N N
30 C3' H3' C H sing 1.09 N N
31 C1' H1' C H sing 1.09 N N
32 C4' H4' C H sing 1.09 N N
33 C5' H5' C H sing 1.09 N N
34 C5' H5'A C H sing 1.09 N N
35 O5' HO5' O H sing 0.97 N N
36 C8 H8 C H sing 1.08 N N
37 N6 HN6 N H sing 0.97 N N
38 N6 HN6A N H sing 0.97 N N
39 C2 H2 C H sing 1.08 N N



3AM : Used in PDB Entries

Total Number of PDB Entries: 11
Ligand Code PDB Entry ID Type Total Distinct
3AM 3agn Open in New Window Bound ligand 1 1
3AM 3ago Open in New Window Bound ligand 1 1
3AM 3c0g Open in New Window Bound ligand 2 1
3AM 3c0i Open in New Window Bound ligand 1 1
3AM 3it3 Open in New Window Bound ligand 2 1
3AM 3ocw Open in New Window Bound ligand 1 1
3AM 3w2v Open in New Window Bound ligand 1 1
3AM 5ldo Open in New Window Bound ligand 1 1
3AM 8iy0 Open in New Window Bound ligand 18 1
3AM 8iy1 Open in New Window Bound ligand 12 1
3AM 8iy2 Open in New Window Bound ligand 22 1