Chemical Components in the PDB

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50T : Summary

Code

50T

One-letter code

X

Molecule name

ADENOSINE-5'-PHOSPHOVANADATE

Systematic names

ProgramVersionName
ACDLabs 12.01 vanadium(5+) hydroxide 5'-O-[(R)-hydroxyphosphinato]adenosine (1:4:1)
OpenEye OEToolkits 1.9.2 [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl]oxy-tetrakis(oxidanyl)vanadium

Formula

C10 H17 N5 O11 P V

Formal charge

0

Molecular weight

465.184 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O[V](O)(O)(O)O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[V](O)(O)(O)O)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 1.9.2 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)O[V](O)(O)(O)O)O)O)N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[V](O)(O)(O)O)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 1.9.2 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O)O[V](O)(O)(O)O)O)O)N

IUPAC InChI

InChI=1S/C10H14N5O7P.4H2O.V/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);4*1H2;/q;;;;;+5/p-5/t4-,6-,7-,10-;;;;;/m1...../s1

IUPAC InChI key

GRUHEBDEJPYXQQ-AZGWGOJFSA-I
50T

wwPDB Information

Atom count

45 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-06-04

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



50T : Atoms of Molecule

Total Number of Atoms: 45
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 -2.804 0.925 -0.459
2 C2 C C2 N Y N 0 -7.105 -0.241 -0.999
3 C2' C C2' R N N 0 -2.942 2.029 0.62
4 C3' C C3' S N N 0 -1.645 2.848 0.414
5 C4 C C4 N Y N 0 -4.917 -0.463 -0.332
6 C4' C C4' R N N 0 -0.698 1.879 -0.319
7 C5 C C5 N Y N 0 -5.219 -1.728 0.199
8 C5' C C5' N N N 0 0.579 1.679 0.5
9 C6 C C6 N Y N 0 -6.539 -2.197 0.087
10 C8 C C8 N Y N 0 -3.112 -1.362 0.562
11 H1' H H1' N N N 0 -3.118 1.299 -1.433
12 H1B H H1B N N N 0 4.506 -2.775 0.801
13 H2 H H2 N N N 0 -7.864 0.354 -1.485
14 H2' H H2' N N N 0 -4.179 3.592 0.975
15 H2B H H2B N N N 0 6.574 -2.04 -2.078
16 H3' H H3' N N N 0 -2.494 4.644 0.022
17 H3B H H3B N N N 0 7.366 -1.148 1.103
18 H4' H H4' N N N 0 -0.449 2.277 -1.303
19 H4B H H4B N N N 0 6.286 1.332 -0.793
20 H5'1 H H5'1 N N N 0 1.032 2.648 0.708
21 H5'2 H H5'2 N N N 0 0.334 1.183 1.439
22 H61N H H61N N N N 0 -6.232 -3.991 1.028
23 H62N H H62N N N N 0 -7.81 -3.748 0.507
24 H8 H H8 N N N 0 -2.093 -1.5 0.89
25 HA H HA N N N 0 -2.973 1.595 1.62
26 HB H HB N N N 0 -1.221 3.143 1.374
27 HOA H HOA N N N 0 2.297 -1.304 1.438
28 N1 N N1 N Y N 0 -7.436 -1.424 -0.515
29 N3 N N3 N Y N 0 -5.882 0.239 -0.917
30 N6 N N6 N N N 0 -6.896 -3.435 0.591
31 N7 N N7 N Y N 0 -4.074 -2.222 0.73
32 N9 N N9 N Y N 0 -3.582 -0.26 -0.088
33 O1A O O1A N N N 0 3.698 1.681 0.697
34 O1B O O1B N N N 0 4.718 -1.865 1.051
35 O2' O O2' N N N 0 -4.098 2.835 0.38
36 O2A O O2A N N N 0 2.779 -0.484 1.612
37 O2B O O2B N N N 0 5.708 -1.622 -1.969
38 O3' O O3' N N N 0 -1.904 4.0 -0.391
39 O3A O O3A N N N 0 3.76 -0.333 -0.823
40 O3B O O3B N N N 0 7.131 -1.398 0.198
41 O4' O O4' N N N 0 -1.391 0.627 -0.457
42 O4B O O4B N N N 0 5.911 0.89 -0.019
43 O5' O O5' N N N 0 1.498 0.873 -0.24
44 PA P PA N N N 0 2.95 0.461 0.32
45 VB V VB N N N 0 5.446 -0.866 -0.312



50T : Chemical Bonds

Total Number of Bonds: 47
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C2 N1 C N sing 1.32 N Y
2 C2 N3 C N doub 1.32 N Y
3 C4 C5 C C doub 1.4 N Y
4 C4 N9 C N sing 1.37 N Y
5 C4 N3 C N sing 1.33 N Y
6 C5 C6 C C sing 1.41 N Y
7 C5 N7 C N sing 1.36 N Y
8 C6 N1 C N doub 1.33 N Y
9 C6 N6 C N sing 1.38 N N
10 C8 N9 C N sing 1.36 N Y
11 C1' N9 C N sing 1.47 N N
12 C8 N7 C N doub 1.3 N Y
13 O3B VB O V sing 1.84 N N
14 O2' C2' O C sing 1.43 N N
15 O2B VB O V sing 1.84 N N
16 O3' C3' O C sing 1.43 N N
17 C3' C4' C C sing 1.54 N N
18 C3' C2' C C sing 1.55 N N
19 C4' C5' C C sing 1.53 N N
20 C4' O4' C O sing 1.44 N N
21 C5' O5' C O sing 1.43 N N
22 O5' PA O P sing 1.61 N N
23 PA O1A P O doub 1.48 N N
24 PA O2A P O sing 1.61 N N
25 PA O3A P O sing 1.61 N N
26 O3A VB O V sing 1.84 N N
27 O1B VB O V sing 1.84 N N
28 O4B VB O V sing 1.84 N N
29 C2' C1' C C sing 1.55 N N
30 C1' O4' C O sing 1.44 N N
31 O2A HOA O H sing 0.97 N N
32 C2 H2 C H sing 1.08 N N
33 N6 H61N N H sing 0.97 N N
34 N6 H62N N H sing 0.97 N N
35 C8 H8 C H sing 1.08 N N
36 O3B H3B O H sing 0.97 N N
37 O2' H2' O H sing 0.97 N N
38 C2' HA C H sing 1.09 N N
39 O3' H3' O H sing 0.97 N N
40 C3' HB C H sing 1.09 N N
41 C4' H4' C H sing 1.09 N N
42 C5' H5'1 C H sing 1.09 N N
43 C5' H5'2 C H sing 1.09 N N
44 O1B H1B O H sing 0.97 N N
45 O2B H2B O H sing 0.97 N N
46 O4B H4B O H sing 0.97 N N
47 C1' H1' C H sing 1.09 N N



50T : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
50T 4bre Open in New Window Bound ligand 2 1