Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

8KI : Summary

Code

8KI

One-letter code

X

Molecule name

(1S,5S,6S)-5-methyl-1-[(1S,2S)-2-methyl-1,2,3-tris(oxidanyl)propyl]-2-oxa-7,9-diazabicyclo[4.2.2]decane-8,10-dione

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (1~{S},5~{S},6~{S})-5-methyl-1-[(1~{S},2~{S})-2-methyl-1,2,3-tris(oxidanyl)propyl]-2-oxa-7,9-diazabicyclo[4.2.2]decane-8,10-dione

Formula

C12 H20 N2 O6

Formal charge

0

Molecular weight

288.297 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH]1CCO[C]2(NC(=O)[CH]1NC2=O)[CH](O)[C](C)(O)CO
SMILES OpenEye OEToolkits 2.0.7 CC1CCOC2(C(=O)NC1C(=O)N2)C(C(C)(CO)O)O
Canonical SMILES CACTVS 3.385 C[C@H]1CCO[C@@]2(NC(=O)[C@H]1NC2=O)[C@@H](O)[C@@](C)(O)CO
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@H]1CCO[C@]2(C(=O)N[C@@H]1C(=O)N2)[C@H]([C@](C)(CO)O)O

IUPAC InChI

InChI=1S/C12H20N2O6/c1-6-3-4-20-12(9(17)11(2,19)5-15)10(18)13-7(6)8(16)14-12/h6-7,9,15,17,19H,3-5H2,1-2H3,(H,13,18)(H,14,16)/t6-,7-,9-,11-,12-/m0/s1

IUPAC InChI key

BXNDMHSEWSMSNI-USYUNJQESA-N
8KI

wwPDB Information

Atom count

40 (20 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-12-20

Last modified at

2023-02-10

Status

Released

Obsoleted

Not Assigned



8KI : Atoms of Molecule

Total Number of Atoms: 40
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C12 C C1 N N N 0 4.422 -1.051 -0.134
2 C09 C C2 S N N 0 3.119 -0.454 -0.669
3 C02 C C3 S N N 0 2.684 0.637 0.263
4 O04 O O2 N N N 0 -0.234 -0.919 -0.792
5 N01 N N1 N N N 0 2.111 -0.006 1.461
6 C01 C C4 N N N 0 0.83 -0.431 1.383
7 O01 O O1 N N N 0 0.388 -1.171 2.236
8 C10 C C5 N N N 0 2.121 -1.584 -0.861
9 C08 C C6 N N N 0 0.917 -1.091 -1.667
10 C04 C C7 S N N 0 -0.037 0.002 0.263
11 N02 N N2 N N N 0 0.365 1.302 -0.302
12 C03 C C8 N N N 0 1.689 1.578 -0.335
13 O02 O O3 N N N 0 2.074 2.603 -0.857
14 C05 C C9 S N N 0 -1.421 0.245 0.87
15 O05 O O4 N N N 0 -1.568 1.633 1.179
16 O03 O O6 N N N 0 -4.887 -0.27 -0.484
17 C06 C C10 S N N 0 -2.498 -0.17 -0.134
18 C11 C C11 N N N 0 -2.32 0.623 -1.431
19 O06 O O5 N N N 0 -2.379 -1.567 -0.41
20 C07 C C12 N N N 0 -3.881 0.117 0.453
21 H1 H H1 N N N 0 4.241 -1.502 0.842
22 H2 H H2 N N N 0 4.784 -1.813 -0.824
23 H3 H H3 N N N 0 5.17 -0.264 -0.037
24 H4 H H4 N N N 0 3.324 -0.01 -1.643
25 H5 H H5 N N N 0 3.561 1.204 0.573
26 H6 H H6 N N N 0 2.632 -0.119 2.271
27 H7 H H7 N N N 0 2.601 -2.405 -1.394
28 H8 H H8 N N N 0 1.781 -1.936 0.113
29 H9 H H9 N N N 0 1.161 -0.137 -2.134
30 H10 H H10 N N N 0 0.676 -1.821 -2.44
31 H11 H H11 N N N 0 -0.292 1.934 -0.636
32 H12 H H12 N N N 0 -1.527 -0.344 1.781
33 H13 H H13 N N N 0 -1.609 2.207 0.402
34 H14 H H14 N N N 0 -1.302 0.493 -1.799
35 H15 H H15 N N N 0 -3.025 0.26 -2.178
36 H16 H H16 N N N 0 -2.505 1.68 -1.239
37 H17 H H17 N N N 0 -2.481 -2.132 0.368
38 H18 H H18 N N N 0 -4.008 -0.447 1.377
39 H19 H H19 N N N 0 -3.972 1.183 0.664
40 H20 H H20 N N N 0 -5.791 -0.116 -0.178



8KI : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O01 C01 O C doub 1.21 N N
2 C11 C06 C C sing 1.53 N N
3 O05 C05 O C sing 1.43 N N
4 C05 C06 C C sing 1.53 N N
5 C05 C04 C C sing 1.53 N N
6 O03 C07 O C sing 1.43 N N
7 C07 C06 C C sing 1.53 N N
8 C06 O06 C O sing 1.43 N N
9 C01 C04 C C sing 1.48 N N
10 C01 N01 C N sing 1.35 N N
11 O04 C08 O C sing 1.46 N N
12 O04 C04 O C sing 1.41 N N
13 C08 C10 C C sing 1.53 N N
14 C04 N02 C N sing 1.47 N N
15 N01 C02 N C sing 1.48 N N
16 N02 C03 N C sing 1.35 N N
17 C10 C09 C C sing 1.52 N N
18 C12 C09 C C sing 1.53 N N
19 C02 C09 C C sing 1.5 N N
20 C02 C03 C C sing 1.49 N N
21 C03 O02 C O doub 1.21 N N
22 C12 H1 C H sing 1.09 N N
23 C12 H2 C H sing 1.09 N N
24 C12 H3 C H sing 1.09 N N
25 C09 H4 C H sing 1.09 N N
26 C02 H5 C H sing 1.09 N N
27 N01 H6 N H sing 0.97 N N
28 C10 H7 C H sing 1.09 N N
29 C10 H8 C H sing 1.09 N N
30 C08 H9 C H sing 1.09 N N
31 C08 H10 C H sing 1.09 N N
32 N02 H11 N H sing 0.97 N N
33 C05 H12 C H sing 1.09 N N
34 O05 H13 O H sing 0.97 N N
35 C11 H14 C H sing 1.09 N N
36 C11 H15 C H sing 1.09 N N
37 C11 H16 C H sing 1.09 N N
38 O06 H17 O H sing 0.97 N N
39 C07 H18 C H sing 1.09 N N
40 C07 H19 C H sing 1.09 N N
41 O03 H20 O H sing 0.97 N N



8KI : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
8KI 7v2u Open in New Window Bound ligand 1 1