Chemical Components in the PDB

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6US : Summary

Code

6US

One-letter code

X

Molecule name

[(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[2-(1~{H}-indol-3-yl)ethyl]phosphonamidic acid

Synonyms

TpAra-Ad

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.5 [(2~{R},3~{S},4~{S},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-~{N}-[2-(1~{H}-indol-3-yl)ethyl]phosphonamidic acid

Formula

C20 H24 N7 O6 P

Formal charge

0

Molecular weight

489.422 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)NCCc4c[nH]c5ccccc45)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 2.0.5 c1ccc2c(c1)c(c[nH]2)CCNP(=O)(O)OCC3C(C(C(O3)n4cnc5c4ncnc5N)O)O
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)NCCc4c[nH]c5ccccc45)[C@@H](O)[C@@H]3O
Canonical SMILES OpenEye OEToolkits 2.0.5 c1ccc2c(c1)c(c[nH]2)CCNP(=O)(O)OC[C@@H]3[C@H]([C@@H]([C@@H](O3)n4cnc5c4ncnc5N)O)O

IUPAC InChI

InChI=1S/C20H24N7O6P/c21-18-15-19(24-9-23-18)27(10-25-15)20-17(29)16(28)14(33-20)8-32-34(30,31)26-6-5-11-7-22-13-4-2-1-3-12(11)13/h1-4,7,9-10,14,16-17,20,22,28-29H,5-6,8H2,(H2,21,23,24)(H2,26,30,31)/t14-,16-,17+,20-/m1/s1

IUPAC InChI key

QUYHGTZYKXLUHM-DFYYWFRZSA-N
6US

wwPDB Information

Atom count

58 (34 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-06-28

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



6US : Atoms of Molecule

Total Number of Atoms: 58
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -2.962 0.772 -0.973
2 C5 C C2 N Y N 0 4.158 -2.216 -0.376
3 C6 C C3 N Y N 0 5.155 -3.194 -0.225
4 C7 C C4 N Y N 0 -4.125 -1.404 -1.217
5 C8 C C5 N Y N 0 2.476 -0.953 -0.902
6 C16 C C6 N Y N 0 -5.163 -1.573 1.198
7 C2 C C7 N Y N 0 6.109 -1.916 1.444
8 C3 C C8 N N N 0 -4.193 0.065 -1.544
9 C12 C C9 N Y N 0 -4.579 -2.043 0.02
10 C14 C C10 N Y N 0 -5.225 -3.807 2.049
11 O3P O O1 N N N 0 -3.673 2.829 1.243
12 P P P1 N N N 0 -2.637 3.14 0.051
13 N1P N N1 N N N 0 -3.028 2.205 -1.292
14 O2P O O2 N N N 0 -2.714 4.574 -0.307
15 O5' O O3 N N N 0 -1.142 2.787 0.534
16 C5' C C11 N N N 0 0.026 3.234 -0.159
17 C4' C C12 R N N 0 1.274 2.724 0.564
18 C3' C C13 S N N 0 2.548 3.297 -0.094
19 O3' O O4 N N N 0 3.027 4.426 0.641
20 C2' C C14 S N N 0 3.564 2.135 -0.022
21 O2' O O5 N N N 0 3.966 1.74 -1.335
22 C1' C C15 R N N 0 2.782 0.997 0.671
23 O4' O O6 N N N 0 1.393 1.293 0.413
24 N9 N N2 N Y N 0 3.145 -0.298 0.089
25 C4 C C16 N Y N 0 4.216 -1.077 0.446
26 N7 N N3 N Y N 0 3.075 -2.075 -1.177
27 N3 N N4 N Y N 0 5.2 -0.971 1.333
28 N1 N N5 N Y N 0 6.099 -3.001 0.69
29 N6 N N6 N N N 0 5.153 -4.334 -1.01
30 C9 C C17 N Y N 0 -3.641 -2.376 -2.006
31 N10 N N7 N Y N 0 -3.745 -3.586 -1.374
32 C11 C C18 N Y N 0 -4.319 -3.418 -0.134
33 C13 C C19 N Y N 0 -4.649 -4.293 0.895
34 C15 C C20 N Y N 0 -5.479 -2.451 2.196
35 H1 H H1 N N N 0 -2.937 0.642 0.109
36 H2 H H2 N N N 0 -2.06 0.344 -1.411
37 H3 H H3 N N N 0 1.584 -0.59 -1.391
38 H4 H H4 N N N 0 -5.364 -0.519 1.319
39 H5 H H5 N N N 0 6.895 -1.799 2.175
40 H6 H H6 N N N 0 -5.094 0.494 -1.106
41 H7 H H7 N N N 0 -4.217 0.196 -2.626
42 H8 H H8 N N N 0 -5.481 -4.489 2.847
43 H9 H H9 N N N 0 -3.677 1.905 1.53
44 H10 H H10 N N N 0 -2.432 2.429 -2.075
45 H11 H H11 N N N 0 0.013 2.849 -1.178
46 H12 H H12 N N N 0 0.039 4.324 -0.182
47 H13 H H13 N N N 0 1.237 2.994 1.62
48 H14 H H14 N N N 0 2.353 3.57 -1.131
49 H15 H H15 N N N 0 3.826 4.826 0.271
50 H16 H H16 N N N 0 4.43 2.421 0.574
51 H17 H H17 N N N 0 4.408 2.437 -1.838
52 H18 H H18 N N N 0 2.98 0.999 1.743
53 H19 H H19 N N N 0 4.458 -4.464 -1.674
54 H20 H H20 N N N 0 5.846 -5.003 -0.896
55 H21 H H21 N N N 0 -3.232 -2.227 -2.994
56 H22 H H22 N N N 0 -3.461 -4.435 -1.746
57 H23 H H23 N N N 0 -4.455 -5.35 0.79
58 H24 H H24 N N N 0 -5.931 -2.086 3.107



6US : Chemical Bonds

Total Number of Bonds: 62
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C15 C14 C C doub 1.39 N Y
2 C15 C16 C C sing 1.37 N Y
3 C14 C13 C C sing 1.38 N Y
4 C16 C12 C C doub 1.4 N Y
5 O2P P O P doub 1.48 N N
6 C13 C11 C C doub 1.39 N Y
7 C12 C11 C C sing 1.41 N Y
8 C12 C7 C C sing 1.46 N Y
9 C1 C3 C C sing 1.53 N N
10 C1 N1P C N sing 1.47 N N
11 C11 N10 C N sing 1.38 N Y
12 C3 C7 C C sing 1.51 N N
13 P N1P P N sing 1.68 N N
14 P O5' P O sing 1.61 N N
15 P O3P P O sing 1.61 N N
16 C7 C9 C C doub 1.34 N Y
17 O5' C5' O C sing 1.43 N N
18 N10 C9 N C sing 1.37 N Y
19 O3' C3' O C sing 1.43 N N
20 C5' C4' C C sing 1.53 N N
21 C4' C3' C C sing 1.54 N N
22 C4' O4' C O sing 1.44 N N
23 C3' C2' C C sing 1.55 N N
24 O4' C1' O C sing 1.44 N N
25 C2' C1' C C sing 1.54 N N
26 C2' O2' C O sing 1.43 N N
27 C1' N9 C N sing 1.47 N N
28 N3 C4 N C doub 1.33 N Y
29 N3 C2 N C sing 1.32 N Y
30 N9 C4 N C sing 1.37 N Y
31 N9 C8 N C sing 1.36 N Y
32 C4 C5 C C sing 1.41 N Y
33 C2 N1 C N doub 1.32 N Y
34 C8 N7 C N doub 1.3 N Y
35 C5 N7 C N sing 1.35 N Y
36 C5 C6 C C doub 1.4 N Y
37 N1 C6 N C sing 1.33 N Y
38 C6 N6 C N sing 1.38 N N
39 C1 H1 C H sing 1.09 N N
40 C1 H2 C H sing 1.09 N N
41 C8 H3 C H sing 1.08 N N
42 C16 H4 C H sing 1.08 N N
43 C2 H5 C H sing 1.08 N N
44 C3 H6 C H sing 1.09 N N
45 C3 H7 C H sing 1.09 N N
46 C14 H8 C H sing 1.08 N N
47 O3P H9 O H sing 0.97 N N
48 N1P H10 N H sing 1.01 N N
49 C5' H11 C H sing 1.09 N N
50 C5' H12 C H sing 1.09 N N
51 C4' H13 C H sing 1.09 N N
52 C3' H14 C H sing 1.09 N N
53 O3' H15 O H sing 0.97 N N
54 C2' H16 C H sing 1.09 N N
55 O2' H17 O H sing 0.97 N N
56 C1' H18 C H sing 1.09 N N
57 N6 H19 N H sing 0.97 N N
58 N6 H20 N H sing 0.97 N N
59 C9 H21 C H sing 1.08 N N
60 N10 H22 N H sing 0.97 N N
61 C13 H23 C H sing 1.08 N N
62 C15 H24 C H sing 1.08 N N



6US : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
6US 5km6 Open in New Window Bound ligand 1 1