Chemical Components in the PDB

pdbe.org/chem
spacer

TR5 : Summary

Code

TR5

One-letter code

X

Molecule name

5-methyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-1,5-dihydro-1,4,5,6,8-pentaazaacenaphthylen-3-amine

Synonyms

Triciribine phosphate

Systematic names

ProgramVersionName
ACDLabs 12.01 5-methyl-1-(5-O-phosphono-beta-D-ribofuranosyl)-1,5-dihydro-1,4,5,6,8-pentaazaacenaphthylen-3-amine

Formula

C13 H17 N6 O7 P

Formal charge

0

Molecular weight

400.284 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)OCC4OC(n1cc2C(=NN(c3ncnc1c23)C)N)C(O)C4O
SMILES CACTVS 3.370 CN1N=C(N)c2cn([CH]3O[CH](CO[P](O)(O)=O)[CH](O)[CH]3O)c4ncnc1c24
SMILES OpenEye OEToolkits 1.7.6 CN1c2c3c(cn(c3ncn2)C4C(C(C(O4)COP(=O)(O)O)O)O)C(=N1)N
Canonical SMILES CACTVS 3.370 CN1N=C(N)c2cn([C@@H]3O[C@H](CO[P](O)(O)=O)[C@@H](O)[C@H]3O)c4ncnc1c24
Canonical SMILES OpenEye OEToolkits 1.7.6 CN1c2c3c(cn(c3ncn2)[C@H]4[C@@H]([C@@H]([C@H](O4)COP(=O)(O)O)O)O)C(=N1)N

IUPAC InChI

InChI=1S/C13H17N6O7P/c1-18-11-7-5(10(14)17-18)2-19(12(7)16-4-15-11)13-9(21)8(20)6(26-13)3-25-27(22,23)24/h2,4,6,8-9,13,20-21H,3H2,1H3,(H2,14,17)(H2,22,23,24)/t6-,8-,9-,13-/m1/s1

IUPAC InChI key

URLYINUFLXOMHP-HTVVRFAVSA-N
TR5

wwPDB Information

Atom count

44 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-07-13

Last modified at

2012-12-28

Status

Released

Obsoleted

Not Assigned



TR5 : Atoms of Molecule

Total Number of Atoms: 44
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2 O O2 N N N 0 -6.343 -0.568 -0.365
2 PB P PB N N N 0 -5.187 -1.302 0.196
3 O3 O O3 N N N 0 -5.636 -2.064 1.541
4 O1 O O1 N N N 0 -4.662 -2.379 -0.881
5 O5' O O5* N N N 0 -4.005 -0.264 0.536
6 C5' C C5* N N N 0 -3.461 0.64 -0.428
7 C4' C C4* R N N 0 -2.361 1.48 0.224
8 O4' O O4* N N N 0 -1.249 0.64 0.577
9 C3' C C3* S N N 0 -1.841 2.53 -0.776
10 O3' O O3* N N N 0 -2.045 3.85 -0.267
11 C2' C C2* R N N 0 -0.329 2.222 -0.9
12 O2' O O2* N N N 0 0.437 3.428 -0.934
13 C1' C C1* R N N 0 -0.052 1.428 0.403
14 N9 N N9 N Y N 0 1.118 0.562 0.241
15 C8 C C8 N Y N 0 1.062 -0.774 -0.122
16 C7 C C7 N Y N 0 2.307 -1.284 -0.184
17 C5 C C5 N Y N 0 3.172 -0.161 0.17
18 C4 C C4 N Y N 0 2.409 0.963 0.42
19 N3 N N3 N Y N 0 3.118 2.046 0.754
20 C2 C C2 N Y N 0 4.435 1.976 0.82
21 N1 N N1 N Y N 0 5.166 0.892 0.578
22 C6 C C6 N Y N 0 4.552 -0.235 0.234
23 N61 N N61 N N N 0 5.123 -1.449 -0.054
24 C62 C C62 N N N 0 6.579 -1.597 0.0040
25 N71 N N71 N N N 0 4.327 -2.549 -0.402
26 C72 C C72 N N N 0 3.02 -2.54 -0.478
27 N73 N N73 N N N 0 2.32 -3.69 -0.829
28 H1 H H1 N N N 0 -6.347 -2.707 1.41
29 H2 H H2 N N N 0 -3.904 -2.898 -0.58
30 H3 H H3 N N N 0 -3.041 0.074 -1.26
31 H4 H H4 N N N 0 -4.249 1.296 -0.796
32 H5 H H5 N N N 0 -2.75 1.973 1.115
33 H6 H H6 N N N 0 -2.334 2.414 -1.742
34 H7 H H7 N N N 0 -1.736 4.551 -0.857
35 H8 H H8 N N N 0 -0.127 1.609 -1.778
36 H9 H H9 N N N 0 0.233 4.002 -1.685
37 H10 H H10 N N N 0 0.089 2.108 1.244
38 H11 H H11 N N N 0 0.156 -1.325 -0.324
39 H12 H H12 N N N 0 4.964 2.876 1.094
40 H13 H H13 N N N 0 6.874 -1.899 1.009
41 H14 H H14 N N N 0 6.896 -2.355 -0.711
42 H15 H H15 N N N 0 7.051 -0.646 -0.242
43 H16 H H16 N N N 0 1.352 -3.67 -0.883
44 H17 H H17 N N N 0 2.8 -4.51 -1.021



TR5 : 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 O2' C2' O C sing 1.43 N N
2 C2 N3 C N doub 1.32 N Y
3 C2 N1 C N sing 1.33 N Y
4 O3' C3' O C sing 1.43 N N
5 N3 C4 N C sing 1.34 N Y
6 N1 C6 N C doub 1.33 N Y
7 C2' C3' C C sing 1.55 N N
8 C2' C1' C C sing 1.55 N N
9 C3' C4' C C sing 1.54 N N
10 C4 C5 C C doub 1.38 N Y
11 C4 N9 C N sing 1.36 N Y
12 C6 C5 C C sing 1.38 N Y
13 C6 N61 C N sing 1.37 N N
14 C62 N61 C N sing 1.46 N N
15 C1' N9 C N sing 1.46 N N
16 C1' O4' C O sing 1.44 N N
17 C5 C7 C C sing 1.46 N Y
18 N9 C8 N C sing 1.39 N Y
19 N61 N71 N N sing 1.4 N N
20 C4' C5' C C sing 1.53 N N
21 C4' O4' C O sing 1.44 N N
22 C5' O5' C O sing 1.43 N N
23 C7 C8 C C doub 1.35 N Y
24 C7 C72 C C sing 1.47 N N
25 N71 C72 N C doub 1.31 N N
26 C72 N73 C N sing 1.39 N N
27 O5' PB O P sing 1.61 N N
28 O2 PB O P doub 1.48 N N
29 O1 PB O P sing 1.61 N N
30 PB O3 P O sing 1.61 N N
31 O3 H1 O H sing 0.97 N N
32 O1 H2 O H sing 0.97 N N
33 C5' H3 C H sing 1.09 N N
34 C5' H4 C H sing 1.09 N N
35 C4' H5 C H sing 1.09 N N
36 C3' H6 C H sing 1.09 N N
37 O3' H7 O H sing 0.97 N N
38 C2' H8 C H sing 1.09 N N
39 O2' H9 O H sing 0.97 N N
40 C1' H10 C H sing 1.09 N N
41 C8 H11 C H sing 1.08 N N
42 C2 H12 C H sing 1.08 N N
43 C62 H13 C H sing 1.09 N N
44 C62 H14 C H sing 1.09 N N
45 C62 H15 C H sing 1.09 N N
46 N73 H16 N H sing 0.97 N N
47 N73 H17 N H sing 0.97 N N



TR5 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
TR5 4fyh Open in New Window Bound ligand 4 1