Chemical Components in the PDB

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0Y0 : Summary

Code

0Y0

One-letter code

X

Molecule name

5'-{[(3S)-3-amino-3-carboxypropyl]amino}-5'-deoxyadenosine

Systematic names

ProgramVersionName
ACDLabs 12.01 5'-{[(3S)-3-amino-3-carboxypropyl]amino}-5'-deoxyadenosine
OpenEye OEToolkits 1.7.6 (2S)-4-[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methylamino]-2-azanyl-butanoic acid

Formula

C14 H21 N7 O5

Formal charge

0

Molecular weight

367.36 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C(N)CCNCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
SMILES CACTVS 3.370 N[CH](CCNC[CH]1O[CH]([CH](O)[CH]1O)n2cnc3c(N)ncnc23)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CNCCC(C(=O)O)N)O)O)N
Canonical SMILES CACTVS 3.370 N[C@@H](CCNC[C@H]1O[C@H]([C@H](O)[C@@H]1O)n2cnc3c(N)ncnc23)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CNCC[C@@H](C(=O)O)N)O)O)N

IUPAC InChI

InChI=1S/C14H21N7O5/c15-6(14(24)25)1-2-17-3-7-9(22)10(23)13(26-7)21-5-20-8-11(16)18-4-19-12(8)21/h4-7,9-10,13,17,22-23H,1-3,15H2,(H,24,25)(H2,16,18,19)/t6-,7+,9+,10+,13+/m0/s1

IUPAC InChI key

WSOGVCAFRBSBRE-WFMPWKQPSA-N
0Y0

wwPDB Information

Atom count

47 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-09-07

Last modified at

2014-02-21

Status

Released

Obsoleted

Not Assigned



0Y0 : Atoms of Molecule

Total Number of Atoms: 47
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O O O N N N 0 6.693 -2.957 -0.185
2 C C C N N N 0 6.957 -1.644 -0.274
3 OXT O OXT N N N 0 7.879 -1.258 -0.953
4 CA C CA S N N 0 6.104 -0.651 0.472
5 N N N N N N 0 6.837 0.614 0.616
6 CB C CB N N N 0 4.81 -0.404 -0.305
7 CAS C CAS N N N 0 3.89 0.506 0.512
8 NAR N NAR N N N 0 2.647 0.743 -0.235
9 CAF C CAF N N N 0 1.738 1.615 0.52
10 CAA C CAA R N N 0 0.457 1.839 -0.287
11 OAE O OAE N N N 0 -0.267 0.603 -0.406
12 CAB C CAB S N N 0 -0.458 2.837 0.447
13 OAH O OAH N N N 0 -0.697 3.988 -0.366
14 CAC C CAC R N N 0 -1.772 2.052 0.674
15 OAI O OAI N N N 0 -2.91 2.883 0.439
16 CAD C CAD R N N 0 -1.672 0.935 -0.397
17 N9 N N9 N Y N 0 -2.475 -0.227 -0.007
18 C8 C C8 N Y N 0 -2.047 -1.292 0.728
19 N7 N N7 N Y N 0 -3.021 -2.141 0.887
20 C5 C C5 N Y N 0 -4.131 -1.676 0.267
21 C4 C C4 N Y N 0 -3.796 -0.439 -0.309
22 N3 N N3 N Y N 0 -4.725 0.235 -0.979
23 C2 C C2 N Y N 0 -5.945 -0.245 -1.101
24 N1 N N1 N Y N 0 -6.308 -1.401 -0.574
25 C6 C C6 N Y N 0 -5.445 -2.148 0.106
26 N6 N N6 N N N 0 -5.835 -3.357 0.655
27 H1 H H1 N N N 0 7.267 -3.555 -0.682
28 H2 H H2 N N N 0 5.865 -1.047 1.459
29 H3 H H3 N N N 0 7.664 0.49 1.181
30 H4 H H4 N N N 0 7.07 1.002 -0.286
31 H6 H H6 N N N 0 5.043 0.074 -1.256
32 H7 H H7 N N N 0 4.309 -1.355 -0.489
33 H8 H H8 N N N 0 3.657 0.028 1.463
34 H9 H H9 N N N 0 4.39 1.457 0.695
35 H10 H H10 N N N 0 2.841 1.127 -1.148
36 H12 H H12 N N N 0 1.49 1.145 1.472
37 H13 H H13 N N N 0 2.223 2.574 0.704
38 H14 H H14 N N N 0 0.706 2.219 -1.278
39 H15 H H15 N N N 0 -0.016 3.13 1.4
40 H16 H H16 N N N 0 -1.268 4.65 0.047
41 H17 H H17 N N N 0 -1.804 1.627 1.677
42 H18 H H18 N N N 0 -2.967 3.648 1.027
43 H19 H H19 N N N 0 -1.985 1.309 -1.372
44 H20 H H20 N N N 0 -1.048 -1.414 1.119
45 H21 H H21 N N N 0 -6.676 0.327 -1.652
46 H22 H H22 N N N 0 -5.198 -3.889 1.159
47 H23 H H23 N N N 0 -6.744 -3.673 0.537



0Y0 : Chemical Bonds

Total Number of Bonds: 49
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OXT C O C doub 1.21 N N
2 C CA C C sing 1.51 N N
3 C O C O sing 1.34 N N
4 CA N C N sing 1.47 N N
5 CA CB C C sing 1.53 N N
6 CB CAS C C sing 1.53 N N
7 CAS NAR C N sing 1.47 N N
8 NAR CAF N C sing 1.47 N N
9 CAF CAA C C sing 1.53 N N
10 CAB CAA C C sing 1.54 N N
11 CAB OAH C O sing 1.43 N N
12 CAB CAC C C sing 1.55 N N
13 CAA OAE C O sing 1.44 N N
14 CAC OAI C O sing 1.43 N N
15 CAC CAD C C sing 1.55 N N
16 OAE CAD O C sing 1.44 N N
17 CAD N9 C N sing 1.47 N N
18 C8 N9 C N sing 1.36 N Y
19 C8 N7 C N doub 1.3 N Y
20 N9 C4 N C sing 1.37 N Y
21 N7 C5 N C sing 1.35 N Y
22 C4 N3 C N doub 1.33 N Y
23 C4 C5 C C sing 1.41 N Y
24 N3 C2 N C sing 1.32 N Y
25 C5 C6 C C doub 1.41 N Y
26 C2 N1 C N doub 1.32 N Y
27 C6 N1 C N sing 1.33 N Y
28 C6 N6 C N sing 1.38 N N
29 O H1 O H sing 0.97 N N
30 CA H2 C H sing 1.09 N N
31 N H3 N H sing 1.01 N N
32 N H4 N H sing 1.01 N N
33 CB H6 C H sing 1.09 N N
34 CB H7 C H sing 1.09 N N
35 CAS H8 C H sing 1.09 N N
36 CAS H9 C H sing 1.09 N N
37 NAR H10 N H sing 1.01 N N
38 CAF H12 C H sing 1.09 N N
39 CAF H13 C H sing 1.09 N N
40 CAA H14 C H sing 1.09 N N
41 CAB H15 C H sing 1.09 N N
42 OAH H16 O H sing 0.97 N N
43 CAC H17 C H sing 1.09 N N
44 OAI H18 O H sing 0.97 N N
45 CAD H19 C H sing 1.09 N N
46 C8 H20 C H sing 1.08 N N
47 C2 H21 C H sing 1.08 N N
48 N6 H22 N H sing 0.97 N N
49 N6 H23 N H sing 0.97 N N



0Y0 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
0Y0 4gom Open in New Window Bound ligand 3 1
0Y0 7p9o Open in New Window Bound ligand 1 1