Chemical Components in the PDB

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E7X : Summary

Code

E7X

One-letter code

X

Molecule name

(2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-hydroxyethyl)amino]-2-azaniumyl-butanoate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (2~{S})-4-[[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl-(2-hydroxyethyl)amino]-2-azaniumyl-butanoate

Formula

C16 H25 N7 O6

Formal charge

0

Molecular weight

411.413 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[CH]3O[CH](CN(CCO)CC[CH]([NH3+])C([O-])=O)[CH](O)[CH]3O
SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(cn2)C3C(C(C(O3)CN(CCC(C(=O)[O-])[NH3+])CCO)O)O)N
Canonical SMILES CACTVS 3.385 Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CN(CCO)CC[C@H]([NH3+])C([O-])=O)[C@@H](O)[C@H]3O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CN(CC[C@@H](C(=O)[O-])[NH3+])CCO)O)O)N

IUPAC InChI

InChI=1S/C16H25N7O6/c17-8(16(27)28)1-2-22(3-4-24)5-9-11(25)12(26)15(29-9)23-7-21-10-13(18)19-6-20-14(10)23/h6-9,11-12,15,24-26H,1-5,17H2,(H,27,28)(H2,18,19,20)/t8-,9+,11+,12+,15+/m0/s1

IUPAC InChI key

OHBJWDDPDJOYBP-OPYVMVOTSA-N
E7X

wwPDB Information

Atom count

54 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-11-14

Last modified at

2019-12-27

Status

Released

Obsoleted

Not Assigned



E7X : Atoms of Molecule

Total Number of Atoms: 54
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 N Y N 0 5.322 -0.783 2.162
2 C5 C C2 N Y N 0 4.492 -1.2 -0.356
3 C6 C C3 N Y N 0 5.713 -1.731 0.094
4 C8 C C4 N Y N 0 2.708 -0.559 -1.408
5 N N N1 N N N 1 -4.489 -0.256 2.485
6 CA C C5 S N N 0 -5.223 -0.437 1.226
7 C C C6 N N N 0 -6.058 -1.689 1.307
8 O O O1 N N N -1 -6.883 -1.928 0.441
9 CB C C7 N N N 0 -4.229 -0.562 0.069
10 CG C C8 N N N 0 -3.467 0.755 -0.092
11 CE C C9 N N N 0 -3.212 0.478 -2.484
12 C5' C C10 N N N 0 -1.6 1.787 -1.238
13 C4' C C11 R N N 0 -0.553 1.644 -0.132
14 O4' O O2 N N N 0 0.291 0.499 -0.384
15 C3' C C12 S N N 0 0.408 2.853 -0.141
16 O3' O O3 N N N 0 0.02 3.809 0.848
17 C2' C C13 R N N 0 1.784 2.242 0.206
18 O2' O O4 N N N 0 2.289 2.803 1.419
19 C1' C C14 R N N 0 1.491 0.735 0.384
20 OXT O O5 N N N 0 -5.909 -2.462 2.237
21 C01 C C15 N N N 0 -2.236 -0.049 -3.537
22 N01 N N2 N N N 0 -2.512 0.636 -1.202
23 N1 N N3 N Y N 0 6.083 -1.492 1.348
24 O01 O O6 N N N 0 -1.816 -1.367 -3.18
25 N3 N N4 N Y N 0 4.168 -0.275 1.787
26 C4 C C16 N Y N 0 3.718 -0.456 0.549
27 N6 N N5 N N N 0 6.513 -2.482 -0.749
28 N7 N N6 N Y N 0 3.814 -1.233 -1.529
29 N9 N N7 N Y N 0 2.599 -0.065 -0.142
30 H1 H H1 N N N 0 5.659 -0.617 3.175
31 H2 H H2 N N N 0 1.979 -0.418 -2.192
32 H3 H H3 N N N 0 -3.929 0.582 2.431
33 H4 H H4 N N N 0 -5.144 -0.174 3.248
34 H6 H H6 N N N 0 -5.871 0.422 1.056
35 H8 H H8 N N N 0 -3.524 -1.366 0.281
36 H9 H H9 N N N 0 -4.768 -0.784 -0.851
37 H10 H H10 N N N 0 -4.172 1.559 -0.304
38 H11 H H11 N N N 0 -2.927 0.978 0.829
39 H12 H H12 N N N 0 -3.606 1.443 -2.804
40 H13 H H13 N N N 0 -4.034 -0.228 -2.364
41 H14 H H14 N N N 0 -2.168 2.705 -1.085
42 H15 H H15 N N N 0 -1.102 1.825 -2.207
43 H16 H H16 N N N 0 -1.039 1.553 0.84
44 H17 H H17 N N N 0 0.431 3.315 -1.128
45 H18 H H18 N N N 0 0.59 4.589 0.886
46 H19 H H19 N N N 0 2.489 2.4 -0.61
47 H20 H H20 N N N 0 2.434 3.759 1.38
48 H21 H H21 N N N 0 1.32 0.504 1.436
49 H22 H H22 N N N 0 -2.729 -0.075 -4.509
50 H24 H H24 N N N 0 6.233 -2.648 -1.663
51 H25 H H25 N N N 0 7.353 -2.843 -0.426
52 H7 H H7 N N N 0 -1.367 0.608 -3.588
53 H23 H H23 N N N 0 -1.194 -1.765 -3.805
54 H5 H H5 N N N 0 -3.888 -1.052 2.642



E7X : Chemical Bonds

Total Number of Bonds: 56
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OXT C O C doub 1.22 N N
2 C O C O sing 1.22 N N
3 C CA C C sing 1.51 N N
4 N6 C6 N C sing 1.38 N N
5 CA N C N sing 1.47 N N
6 CA CB C C sing 1.53 N N
7 N1 C6 N C doub 1.33 N Y
8 N1 C2 N C sing 1.32 N Y
9 C6 C5 C C sing 1.41 N Y
10 C2 N3 C N doub 1.32 N Y
11 C5 N7 C N sing 1.36 N Y
12 C5 C4 C C doub 1.4 N Y
13 N7 C8 N C doub 1.3 N Y
14 N3 C4 N C sing 1.33 N Y
15 C4 N9 C N sing 1.37 N Y
16 CB CG C C sing 1.53 N N
17 C8 N9 C N sing 1.36 N Y
18 N9 C1' N C sing 1.46 N N
19 CG N01 C N sing 1.47 N N
20 C1' O4' C O sing 1.44 N N
21 C1' C2' C C sing 1.55 N N
22 O4' C4' O C sing 1.44 N N
23 O2' C2' O C sing 1.43 N N
24 C2' C3' C C sing 1.55 N N
25 C4' C5' C C sing 1.53 N N
26 C4' C3' C C sing 1.54 N N
27 N01 C5' N C sing 1.47 N N
28 N01 CE N C sing 1.47 N N
29 O01 C01 O C sing 1.43 N N
30 CE C01 C C sing 1.53 N N
31 C3' O3' C O sing 1.43 N N
32 C2 H1 C H sing 1.08 N N
33 C8 H2 C H sing 1.08 N N
34 N H3 N H sing 1.01 N N
35 N H4 N H sing 1.01 N N
36 CA H6 C H sing 1.09 N N
37 CB H8 C H sing 1.09 N N
38 CB H9 C H sing 1.09 N N
39 CG H10 C H sing 1.09 N N
40 CG H11 C H sing 1.09 N N
41 CE H12 C H sing 1.09 N N
42 CE H13 C H sing 1.09 N N
43 C5' H14 C H sing 1.09 N N
44 C5' H15 C H sing 1.09 N N
45 C4' H16 C H sing 1.09 N N
46 C3' H17 C H sing 1.09 N N
47 O3' H18 O H sing 0.97 N N
48 C2' H19 C H sing 1.09 N N
49 O2' H20 O H sing 0.97 N N
50 C1' H21 C H sing 1.09 N N
51 C01 H22 C H sing 1.09 N N
52 N6 H24 N H sing 0.97 N N
53 N6 H25 N H sing 0.97 N N
54 C01 H7 C H sing 1.09 N N
55 O01 H23 O H sing 0.97 N N
56 N H5 N H sing 1.01 N N



E7X : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
E7X 6laz Open in New Window Bound ligand 2 1