Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

7TE : Summary

Code

7TE

One-letter code

X

Molecule name

(S)-({[(3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxyoxolan-3-yl]oxy}methyl)phosphinic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 ({[(3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxyoxolan-3-yl]oxy}methyl)phosphonic acid
OpenEye OEToolkits 2.0.7 [(3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-4-oxidanyl-oxolan-3-yl]oxymethylphosphonic acid

Formula

C10 H14 N5 O6 P

Formal charge

0

Molecular weight

331.222 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=P(O)(O)COC1COC(n2cnc3c(N)ncnc32)C1O
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3OC[CH](OC[P](O)(O)=O)[CH]3O
SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(cn2)C3C(C(CO3)OCP(=O)(O)O)O)N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3OC[C@H](OC[P](O)(O)=O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H](CO3)OCP(=O)(O)O)O)N

IUPAC InChI

InChI=1S/C10H14N5O6P/c11-8-6-9(13-2-12-8)15(3-14-6)10-7(16)5(1-20-10)21-4-22(17,18)19/h2-3,5,7,10,16H,1,4H2,(H2,11,12,13)(H2,17,18,19)/t5-,7+,10+/m0/s1

IUPAC InChI key

BXHBMXLCBPCKJC-WVBSTYLSSA-N
7TE

wwPDB Information

Atom count

36 (22 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-08-19

Last modified at

2022-08-24

Status

Released

Obsoleted

Not Assigned



7TE : Atoms of Molecule

Total Number of Atoms: 36
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 -0.658 -1.621 0.103
2 C2 C C2 N Y N 0 -4.336 -0.026 -1.917
3 C2' C C3 R N N 0 0.43 -0.855 -0.675
4 C3' C C4 S N N 0 1.724 -1.109 0.135
5 C4 C C5 N Y N 0 -2.794 -0.305 -0.235
6 C4' C C6 N N N 0 1.363 -2.387 0.934
7 C5 C C7 N Y N 0 -3.531 0.578 0.572
8 C6 C C8 N Y N 0 -4.705 1.14 0.041
9 C8 C C9 N Y N 0 -1.812 -0.07 1.725
10 CP C C10 N N N 0 3.387 0.19 1.272
11 N1 N N1 N Y N 0 -5.061 0.809 -1.196
12 N3 N N2 N Y N 0 -3.23 -0.576 -1.462
13 N6 N N3 N N N 0 -5.471 2.016 0.788
14 N7 N N4 N Y N 0 -2.877 0.678 1.754
15 N9 N N5 N Y N 0 -1.717 -0.697 0.518
16 O1P O O1 N N N 0 3.517 2.263 -0.46
17 O2' O O2 N N N 0 0.558 -1.377 -1.999
18 O2P O O3 N N N 0 5.733 1.194 0.105
19 O3' O O4 N N N 0 1.997 -0.016 1.015
20 O4' O O5 N N N 0 -0.031 -2.197 1.261
21 P P P1 N N N 0 4.166 0.961 -0.184
22 H1 H H1 N N N 0 -1.078 -2.408 -0.524
23 H2 H H2 N N N 0 -4.664 -0.271 -2.916
24 H3 H H3 N N N 0 0.199 0.209 -0.706
25 H4 H H4 N N N 0 2.569 -1.291 -0.529
26 H5 H H5 N N N 0 1.495 -3.275 0.316
27 H6 H H6 N N N 0 1.964 -2.455 1.84
28 H7 H H7 N N N 0 -1.108 -0.177 2.537
29 H8 H H8 N N N 0 3.504 0.845 2.136
30 H9 H H9 N N N 0 3.865 -0.768 1.475
31 H10 H H10 N N N 0 -5.2 2.25 1.69
32 H11 H H11 N N N 0 -6.279 2.398 0.41
33 H12 H H12 N N Y 0 1.229 -0.931 -2.534
34 H13 H H13 N N N 0 6.212 1.602 -0.629
35 H14 H H14 N N Y 0 4.396 -0.878 -1.35
36 O3P O O6 N N Y 0 3.994 -0.005 -1.46



7TE : Chemical Bonds

Total Number of Bonds: 38
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4' O4' C O sing 1.44 N N
2 C4' C3' C C sing 1.55 N N
3 O4' C1' O C sing 1.44 N N
4 O3' C3' O C sing 1.43 N N
5 O3' CP O C sing 1.43 N N
6 O1P P O P doub 1.48 N N
7 C2 N3 C N doub 1.32 N Y
8 C2 N1 C N sing 1.32 N Y
9 N3 C4 N C sing 1.33 N Y
10 N1 C6 N C doub 1.33 N Y
11 C3' C2' C C sing 1.55 N N
12 C1' N9 C N sing 1.47 N N
13 C1' C2' C C sing 1.54 N N
14 C4 N9 C N sing 1.37 N Y
15 C4 C5 C C doub 1.41 N Y
16 C6 C5 C C sing 1.41 N Y
17 C6 N6 C N sing 1.38 N N
18 N9 C8 N C sing 1.36 N Y
19 C5 N7 C N sing 1.35 N Y
20 P CP P C sing 1.82 N N
21 P O2P P O sing 1.61 N N
22 C8 N7 C N doub 1.3 N Y
23 C2' O2' C O sing 1.43 N N
24 C1' H1 C H sing 1.09 N N
25 C2 H2 C H sing 1.08 N N
26 C2' H3 C H sing 1.09 N N
27 C3' H4 C H sing 1.09 N N
28 C4' H5 C H sing 1.09 N N
29 C4' H6 C H sing 1.09 N N
30 C8 H7 C H sing 1.08 N N
31 CP H8 C H sing 1.09 N N
32 CP H9 C H sing 1.09 N N
33 N6 H10 N H sing 0.97 N N
34 N6 H11 N H sing 0.97 N N
35 O2' H12 O H sing 0.97 N N
36 O2P H13 O H sing 0.97 N N
37 P O3P P O sing 1.61 N N
38 O3P H14 O H sing 0.97 N N



7TE : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
7TE 7rsr Open in New Window Polymer component 2 2
7TE 7tqw Open in New Window Polymer component 2 2