Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

EOI : Summary

Code

EOI

One-letter code

X

Molecule name

[[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-sulfanyl-phosphoryl] phosphono hydrogen phosphate

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.6 [[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-sulfanyl-phosphoryl] phosphono hydrogen phosphate

Formula

C9 H16 N5 O9 P3 S

Formal charge

0

Molecular weight

463.238 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH](Cn1cnc2c(N)ncnc12)OC[P](S)(=O)O[P](O)(=O)O[P](O)(O)=O
SMILES OpenEye OEToolkits 1.7.6 CC(Cn1cnc2c1ncnc2N)OCP(=O)(OP(=O)(O)OP(=O)(O)O)S
Canonical SMILES CACTVS 3.385 C[C@H](Cn1cnc2c(N)ncnc12)OC[P@@](S)(=O)O[P](O)(=O)O[P](O)(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 C[C@H](Cn1cnc2c1ncnc2N)OC[P@@](=O)(OP(=O)(O)OP(=O)(O)O)S

IUPAC InChI

InChI=1S/C9H16N5O9P3S/c1-6(2-14-4-13-7-8(10)11-3-12-9(7)14)21-5-24(15,27)22-26(19,20)23-25(16,17)18/h3-4,6H,2,5H2,1H3,(H,15,27)(H,19,20)(H2,10,11,12)(H2,16,17,18)/t6-,24-/m1/s1

IUPAC InChI key

BMDSOWJDBWVWQG-FMWWOLKHSA-N
EOI

wwPDB Information

Atom count

43 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-01-31

Last modified at

2015-02-06

Status

Released

Obsoleted

Not Assigned



EOI : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 -2.747 4.247 0.373
2 N N N N Y N 0 -3.972 0.83 -0.709
3 O O O N N N 0 -2.197 2.052 1.222
4 P P P R N N 0 -0.064 0.836 0.188
5 S S S N N N 0 -0.68 -1.118 0.733
6 C1 C C1 R N N 0 -2.671 2.75 0.069
7 N1 N N1 N Y N 0 -3.792 -0.934 -1.982
8 O1 O O1 N N N 0 -0.534 1.137 -1.183
9 P1 P P1 N N N 0 2.73 0.15 -0.528
10 C2 C C2 N N N 0 -4.063 2.234 -0.303
11 N2 N N2 N Y N 0 -4.074 -0.434 1.439
12 O2 O O2 N N N 0 1.543 0.925 0.236
13 P2 P P2 N N N 0 5.522 -0.444 0.271
14 C3 C C3 N Y N 0 -3.854 0.366 -1.986
15 N3 N N3 N Y N 0 -3.949 -2.731 1.217
16 O3 O O3 N N N 0 2.386 -1.285 -0.646
17 C4 C C4 N Y N 0 -3.867 -1.385 -0.707
18 N4 N N4 N N N 0 -3.739 -3.801 -0.874
19 O4 O O4 N N N 0 2.922 0.779 -1.997
20 C5 C C5 N Y N 0 -3.983 -0.259 0.125
21 O5 O O5 N N N 0 4.098 0.307 0.307
22 C6 C C6 N Y N 0 -4.056 -1.643 1.959
23 O6 O O6 N N N 0 6.408 0.143 -0.938
24 C7 C C7 N Y N 0 -3.851 -2.656 -0.106
25 O7 O O7 N N N 0 6.29 -0.203 1.666
26 C8 C C8 N N N 0 -0.774 2.045 1.353
27 O8 O O8 N N N 0 5.31 -1.894 0.069
28 H H H N N N 0 -1.775 4.596 0.722
29 HA H HA N N N 0 -3.024 4.788 -0.531
30 HB H HB N N N 0 -3.495 4.424 1.146
31 HS H HS N N N 0 -0.192 -1.252 1.979
32 H1 H H1 N N N 0 -1.988 2.582 -0.763
33 H2 H H2 N N N 0 -4.462 2.826 -1.127
34 H2A H H2A N N N 0 -4.725 2.32 0.56
35 H3 H H3 N N N 0 -3.817 0.986 -2.869
36 HN4 H HN4 N N N 0 -3.73 -4.672 -0.447
37 HN4A H HN4A N N N 0 -3.669 -3.733 -1.839
38 HO6 H HO6 N N N 0 6.586 1.091 -0.871
39 HO4 H HO4 N N N 0 3.15 1.718 -1.997
40 H6 H H6 N N N 0 -4.131 -1.75 3.031
41 HO7 H HO7 N N N 0 7.157 -0.627 1.715
42 H8 H H8 N N N 0 -0.384 3.038 1.13
43 H8A H H8A N N N 0 -0.504 1.769 2.372



EOI : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C C1 C C sing 1.53 N N
2 C H C H sing 1.09 N N
3 C HA C H sing 1.09 N N
4 C HB C H sing 1.09 N N
5 C2 N C N sing 1.46 N N
6 N C3 N C sing 1.36 N Y
7 N C5 N C sing 1.37 N Y
8 C8 O C O sing 1.43 N N
9 O C1 O C sing 1.43 N N
10 C8 P C P sing 1.82 N N
11 S P S P sing 2.12 N N
12 P O2 P O sing 1.61 N N
13 P O1 P O doub 1.48 N N
14 S HS S H sing 1.34 N N
15 C1 C2 C C sing 1.53 N N
16 C1 H1 C H sing 1.09 N N
17 C3 N1 C N doub 1.3 N Y
18 N1 C4 N C sing 1.35 N Y
19 O5 P1 O P sing 1.61 N N
20 O3 P1 O P doub 1.48 N N
21 O2 P1 O P sing 1.61 N N
22 P1 O4 P O sing 1.61 N N
23 C2 H2 C H sing 1.09 N N
24 C2 H2A C H sing 1.09 N N
25 N2 C5 N C sing 1.33 N Y
26 N2 C6 N C doub 1.32 N Y
27 O8 P2 O P doub 1.48 N N
28 O6 P2 O P sing 1.61 N N
29 P2 O7 P O sing 1.61 N N
30 P2 O5 P O sing 1.61 N N
31 C3 H3 C H sing 1.08 N N
32 C6 N3 C N sing 1.32 N Y
33 N3 C7 N C doub 1.33 N Y
34 C5 C4 C C doub 1.4 N Y
35 C4 C7 C C sing 1.41 N Y
36 C7 N4 C N sing 1.38 N N
37 N4 HN4 N H sing 0.97 N N
38 N4 HN4A N H sing 0.97 N N
39 O4 HO4 O H sing 0.97 N N
40 C6 H6 C H sing 1.08 N N
41 O6 HO6 O H sing 0.97 N N
42 O7 HO7 O H sing 0.97 N N
43 C8 H8 C H sing 1.09 N N
44 C8 H8A C H sing 1.09 N N



EOI : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
EOI 4cp5 Open in New Window Bound ligand 6 1