Chemical Components in the PDB

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RV8 : Summary

Code

RV8

One-letter code

X

Molecule name

Triglycidyl isocyanurate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 1,3,5-tris[[(2~{S})-oxiran-2-yl]methyl]-1,3,5-triazinane-2,4,6-trione

Formula

C12 H15 N3 O6

Formal charge

0

Molecular weight

297.264 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 O=C1N(C[CH]2CO2)C(=O)N(C[CH]3CO3)C(=O)N1C[CH]4CO4
SMILES OpenEye OEToolkits 2.0.7 C1C(O1)CN2C(=O)N(C(=O)N(C2=O)CC3CO3)CC4CO4
Canonical SMILES CACTVS 3.385 O=C1N(C[C@H]2CO2)C(=O)N(C[C@H]3CO3)C(=O)N1C[C@H]4CO4
Canonical SMILES OpenEye OEToolkits 2.0.7 C1[C@@H](O1)CN2C(=O)N(C(=O)N(C2=O)C[C@H]3CO3)C[C@H]4CO4

IUPAC InChI

InChI=1S/C12H15N3O6/c16-10-13(1-7-4-19-7)11(17)15(3-9-6-21-9)12(18)14(10)2-8-5-20-8/h7-9H,1-6H2/t7-,8-,9-/m0/s1

IUPAC InChI key

OUPZKGBUJRBPGC-CIUDSAMLSA-N
RV8

wwPDB Information

Atom count

36 (21 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-10-22

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



RV8 : 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 N10 N N1 N N N 0 0.399 1.284 0.728
2 C11 C C1 N N N 0 0.837 2.682 0.728
3 C12 C C2 S N N 0 0.997 3.166 -0.715
4 C13 C C3 N N N 0 1.45 4.611 -0.935
5 C18 C C4 N N N 0 -2.748 -0.617 0.731
6 C19 C C5 S N N 0 -3.243 -0.736 -0.712
7 C20 C C6 N N N 0 -4.727 -1.036 -0.934
8 C02 C C7 N N N 0 -0.406 -1.289 0.728
9 C04 C C8 N N N 0 1.901 -2.072 0.73
10 C05 C C9 S N N 0 2.251 -2.437 -0.714
11 C06 C C10 N N N 0 3.277 -3.55 -0.94
12 C08 C C11 N N N 0 1.312 0.292 0.734
13 C15 C C12 N N N 0 -0.916 0.989 0.726
14 N03 N N2 N N N 0 0.909 -0.994 0.734
15 N17 N N3 N N N 0 -1.319 -0.297 0.732
16 O01 O O1 N N N 0 -0.769 -2.449 0.728
17 O07 O O2 N N N 0 1.881 -3.736 -1.181
18 O09 O O3 N N N 0 2.497 0.557 0.74
19 O16 O O5 N N N 0 -1.739 1.883 0.721
20 O14 O O4 N N N 0 2.313 3.494 -1.164
21 O21 O O6 N N N 0 -4.16 0.254 -1.184
22 H112 H H1 N N N 0 0.093 3.295 1.237
23 H111 H H2 N N N 0 1.792 2.763 1.247
24 H121 H H3 N N N 0 0.305 2.735 -1.438
25 H131 H H4 N N N 0 1.06 5.138 -1.806
26 H132 H H5 N N N 0 1.637 5.225 -0.054
27 H182 H H6 N N N 0 -3.298 0.174 1.24
28 H181 H H7 N N N 0 -2.909 -1.563 1.249
29 H191 H H8 N N N 0 -2.53 -1.148 -1.424
30 H201 H H9 N N N 0 -4.999 -1.647 -1.794
31 H202 H H10 N N N 0 -5.36 -1.15 -0.054
32 H041 H H11 N N N 0 1.491 -2.946 1.236
33 H042 H H12 N N N 0 2.8 -1.741 1.249
34 H051 H H13 N N N 0 2.229 -1.614 -1.429
35 H062 H H14 N N N 0 3.936 -3.466 -1.804
36 H061 H H15 N N N 0 3.71 -4.028 -0.061



RV8 : Chemical Bonds

Total Number of Bonds: 39
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C20 O21 C O sing 1.43 N N
2 C20 C19 C C sing 1.53 N N
3 O21 C19 O C sing 1.43 N N
4 C19 C18 C C sing 1.53 N N
5 C18 N17 C N sing 1.46 N N
6 O16 C15 O C doub 1.22 N N
7 C15 N17 C N sing 1.35 N N
8 C15 N10 C N sing 1.35 N N
9 N17 C02 N C sing 1.35 N N
10 C11 N10 C N sing 1.47 N N
11 C11 C12 C C sing 1.53 N N
12 N10 C08 N C sing 1.35 N N
13 C02 O01 C O doub 1.22 N N
14 C02 N03 C N sing 1.35 N N
15 O07 C05 O C sing 1.43 N N
16 O07 C06 O C sing 1.43 N N
17 C08 N03 C N sing 1.35 N N
18 C08 O09 C O doub 1.21 N N
19 N03 C04 N C sing 1.46 N N
20 C12 C13 C C sing 1.53 N N
21 C12 O14 C O sing 1.43 N N
22 C13 O14 C O sing 1.43 N N
23 C05 C04 C C sing 1.53 N N
24 C05 C06 C C sing 1.53 N N
25 C11 H112 C H sing 1.09 N N
26 C11 H111 C H sing 1.09 N N
27 C12 H121 C H sing 1.09 N N
28 C13 H131 C H sing 1.09 N N
29 C13 H132 C H sing 1.09 N N
30 C18 H182 C H sing 1.09 N N
31 C18 H181 C H sing 1.09 N N
32 C19 H191 C H sing 1.09 N N
33 C20 H201 C H sing 1.09 N N
34 C20 H202 C H sing 1.09 N N
35 C04 H041 C H sing 1.09 N N
36 C04 H042 C H sing 1.09 N N
37 C05 H051 C H sing 1.09 N N
38 C06 H062 C H sing 1.09 N N
39 C06 H061 C H sing 1.09 N N



RV8 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
RV8 7aqj Open in New Window Bound ligand 1 1