Chemical Components in the PDB

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ET9 : Summary

Code

ET9

One-letter code

X

Molecule name

[[(1R,3S,5S)-3-(2-azanyl-6-oxidanylidene-3H-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphory l] phosphono hydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 [[(1~{R},3~{S},5~{S})-3-(2-azanyl-6-oxidanylidene-3~{H}-purin-9-yl)-2-methylidene-5-oxidanyl-cyclopentyl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate

Formula

C12 H18 N5 O12 P3

Formal charge

0

Molecular weight

517.219 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 NC1=NC(=O)c2ncn([CH]3C[CH](O)[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C3=C)c2N1
SMILES OpenEye OEToolkits 2.0.6 C=C1C(CC(C1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)n2cnc3c2NC(=NC3=O)N
Canonical SMILES CACTVS 3.385 NC1=NC(=O)c2ncn([C@H]3C[C@H](O)[C@@H](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)C3=C)c2N1
Canonical SMILES OpenEye OEToolkits 2.0.6 C=C1[C@H](C[C@@H]([C@H]1COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)n2cnc3c2NC(=NC3=O)N

IUPAC InChI

InChI=1S/C12H18N5O12P3/c1-5-6(3-27-31(23,24)29-32(25,26)28-30(20,21)22)8(18)2-7(5)17-4-14-9-10(17)15-12(13)16-11(9)19/h4,6-8,18H,1-3H2,(H,23,24)(H,25,26)(H2,20,21,22)(H3,13,15,16,19)/t6-,7-,8-/m0/s1

IUPAC InChI key

YMBBDUCQYPKKJK-FXQIFTODSA-N
ET9

wwPDB Information

Atom count

50 (32 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-05-30

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



ET9 : Atoms of Molecule

Total Number of Atoms: 50
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1' C C1 S N N 0 3.522 -1.409 -1.272
2 C2 C C2 N N N 0 6.731 1.804 -1.322
3 C2' C C3 N N N 0 3.75 -2.902 -0.927
4 C3' C C4 S N N 0 2.606 -3.187 0.079
5 C4 C C5 N Y N 0 5.069 0.383 -0.407
6 C4' C C6 R N N 0 1.422 -2.363 -0.469
7 C44 C C7 N N N 0 1.344 -0.339 -1.971
8 C5 C C8 N Y N 0 5.295 0.951 0.841
9 C5' C C9 N N N 0 0.621 -1.764 0.689
10 C6 C C10 N N N 0 6.319 1.995 0.95
11 C6' C C11 N N N 0 2.012 -1.257 -1.318
12 C8 C C12 N Y N 0 3.746 -0.54 1.086
13 N1 N N1 N N N 0 6.979 2.365 -0.158
14 N2 N N2 N N N 0 7.44 2.219 -2.418
15 N3 N N3 N N N 0 5.801 0.826 -1.478
16 N7 N N4 N Y N 0 4.458 0.349 1.718
17 N9 N N5 N Y N 0 4.094 -0.55 -0.233
18 O1A O O1 N N N 0 -0.909 0.9 1.837
19 O1B O O2 N N N 0 -4.907 -0.141 1.637
20 O1G O O3 N N N 0 -7.114 0.815 -2.599
21 O2A O O4 N N N 0 -2.108 -1.3 2.141
22 O2B O O5 N N N 0 -4.265 2.22 1.02
23 O2G O O6 N N N 0 -7.507 -0.771 -0.539
24 O3' O O7 N N N 0 2.285 -4.579 0.094
25 O3A O O8 N N N 0 -2.843 0.16 0.217
26 O3B O O9 N N N 0 -5.249 0.558 -0.764
27 O3G O O10 N N N 0 -7.426 1.737 -0.271
28 O5' O O11 N N N 0 -0.537 -1.102 0.175
29 O6 O O12 N N N 0 6.556 2.527 2.024
30 PA P P1 N N N 0 -1.61 -0.356 1.115
31 PB P P2 N N N 0 -4.329 0.681 0.551
32 PG P P3 N N N 0 -6.837 0.61 -1.026
33 H1 H H1 N N N 0 3.958 -1.173 -2.243
34 H2 H H2 N N N 0 3.649 -3.525 -1.815
35 H3 H H3 N N N 0 4.723 -3.047 -0.458
36 H4 H H4 N N N 0 2.881 -2.848 1.078
37 H5 H H5 N N N 0 0.778 -2.997 -1.078
38 H6 H H6 N N N 0 1.872 0.405 -2.549
39 H7 H H7 N N N 0 0.265 -0.327 -1.933
40 H8 H H8 N N N 0 0.313 -2.559 1.368
41 H9 H H9 N N N 0 1.241 -1.046 1.226
42 H10 H H10 N N N 0 2.996 -1.172 1.538
43 H11 H H11 N N N 0 7.274 1.816 -3.284
44 H12 H H12 N N N 0 8.108 2.916 -2.327
45 H13 H H13 N N N 0 5.653 0.438 -2.355
46 H14 H H14 N N N 0 -0.559 1.561 1.224
47 H15 H H15 N N N 0 -8.052 0.855 -2.831
48 H16 H H16 N N N 0 -3.895 2.818 0.356
49 H17 H H17 N N N 0 -7.168 -1.554 -0.993
50 H18 H H18 N N N 0 3.016 -5.148 0.369



ET9 : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O6 C6 O C doub 1.22 N N
2 C6 C5 C C sing 1.47 N N
3 C6 N1 C N sing 1.34 N N
4 N7 C5 N C sing 1.35 N Y
5 N7 C8 N C doub 1.3 N Y
6 C5 C4 C C doub 1.39 N Y
7 N1 C2 N C doub 1.32 N N
8 C44 C6' C C doub 1.31 N N
9 C8 N9 C N sing 1.36 N Y
10 C4 N9 C N sing 1.36 N Y
11 C4 N3 C N sing 1.37 N N
12 C2 N3 C N sing 1.36 N N
13 C2 N2 C N sing 1.37 N N
14 N9 C1' N C sing 1.46 N N
15 C6' C1' C C sing 1.52 N N
16 C6' C4' C C sing 1.51 N N
17 C1' C2' C C sing 1.55 N N
18 O2A PA O P doub 1.48 N N
19 O5' C5' O C sing 1.43 N N
20 O5' PA O P sing 1.61 N N
21 C5' C4' C C sing 1.53 N N
22 PA O1A P O sing 1.61 N N
23 PA O3A P O sing 1.61 N N
24 C4' C3' C C sing 1.54 N N
25 C2' C3' C C sing 1.55 N N
26 C3' O3' C O sing 1.43 N N
27 O3A PB O P sing 1.61 N N
28 O1B PB O P doub 1.48 N N
29 PB O2B P O sing 1.61 N N
30 PB O3B P O sing 1.61 N N
31 O3G PG O P doub 1.48 N N
32 O1G PG O P sing 1.61 N N
33 O3B PG O P sing 1.61 N N
34 PG O2G P O sing 1.61 N N
35 C1' H1 C H sing 1.09 N N
36 C2' H2 C H sing 1.09 N N
37 C2' H3 C H sing 1.09 N N
38 C3' H4 C H sing 1.09 N N
39 C4' H5 C H sing 1.09 N N
40 C44 H6 C H sing 1.08 N N
41 C44 H7 C H sing 1.08 N N
42 C5' H8 C H sing 1.09 N N
43 C5' H9 C H sing 1.09 N N
44 C8 H10 C H sing 1.08 N N
45 N2 H11 N H sing 0.97 N N
46 N2 H12 N H sing 0.97 N N
47 N3 H13 N H sing 0.97 N N
48 O1A H14 O H sing 0.97 N N
49 O1G H15 O H sing 0.97 N N
50 O2B H16 O H sing 0.97 N N
51 O2G H17 O H sing 0.97 N N
52 O3' H18 O H sing 0.97 N N



ET9 : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
ET9 5xn1 Open in New Window Bound ligand 2 1
ET9 6ika Open in New Window Bound ligand 2 1
ET9 6kdm Open in New Window Bound ligand 2 1
ET9 8x21 Open in New Window Bound ligand 2 1