Chemical Components in the PDB

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F5F : Summary

Code

F5F

One-letter code

X

Molecule name

3-[(1R,2S,4R,6S)-2-ethenyl-4,6-dimethyl-cyclohexyl]-4-oxidanyl-1H-pyridin-2-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 3-[(1~{R},2~{S},4~{R},6~{S})-2-ethenyl-4,6-dimethyl-cyclohexyl]-4-oxidanyl-1~{H}-pyridin-2-one

Formula

C15 H21 N O2

Formal charge

0

Molecular weight

247.333 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH]1C[CH](C)[CH]([CH](C1)C=C)C2=C(O)C=CNC2=O
SMILES OpenEye OEToolkits 2.0.7 CC1CC(C(C(C1)C=C)C2=C(C=CNC2=O)O)C
Canonical SMILES CACTVS 3.385 C[C@@H]1C[C@H](C)[C@H]([C@@H](C1)C=C)C2=C(O)C=CNC2=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@@H]1C[C@@H]([C@H]([C@@H](C1)C=C)C2=C(C=CNC2=O)O)C

IUPAC InChI

InChI=1S/C15H21NO2/c1-4-11-8-9(2)7-10(3)13(11)14-12(17)5-6-16-15(14)18/h4-6,9-11,13H,1,7-8H2,2-3H3,(H2,16,17,18)/t9-,10+,11-,13-/m1/s1

IUPAC InChI key

SWIJWROLKBJDFO-LSCVPOLPSA-N
F5F

wwPDB Information

Atom count

39 (18 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-03-31

Last modified at

2020-10-09

Status

Released

Obsoleted

Not Assigned



F5F : Atoms of Molecule

Total Number of Atoms: 39
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 3.36 -0.324 0.747
2 C2 C C2 N N N 0 3.723 -0.135 -0.54
3 C4 C C3 N N N 0 1.473 -0.007 -1.223
4 C5 C C4 N N N 0 1.048 -0.193 0.097
5 C6 C C5 N N N 0 1.994 -0.359 1.092
6 C7 C C6 R N N 0 -0.422 -0.225 0.429
7 C10 C C7 S N N 0 -1.092 -1.37 -0.333
8 C11 C C8 N N N 0 -2.584 -1.402 0.004
9 C12 C C9 R N N 0 -3.227 -0.074 -0.401
10 C13 C C10 N N N 0 -2.557 1.071 0.362
11 C14 C C11 S N N 0 -1.065 1.103 0.025
12 C15 C C12 N N N 0 -0.449 -2.698 0.071
13 C16 C C13 N N N 0 -4.72 -0.106 -0.064
14 C17 C C14 N N N 0 -0.405 2.23 0.776
15 C18 C C15 N N N 0 0.199 3.19 0.12
16 N3 N N1 N N N 0 2.787 0.022 -1.513
17 O8 O O1 N N N 0 1.614 -0.553 2.377
18 O9 O O2 N N N 0 0.649 0.141 -2.113
19 H1 H H1 N N N 0 4.114 -0.451 1.509
20 H2 H H2 N N N 0 4.771 -0.108 -0.8
21 H4 H H4 N N N 0 -0.549 -0.379 1.501
22 H5 H H5 N N N 0 -0.965 -1.216 -1.405
23 H6 H H6 N N N 0 -3.062 -2.217 -0.54
24 H7 H H7 N N N 0 -2.711 -1.556 1.075
25 H8 H H8 N N N 0 -3.1 0.08 -1.472
26 H9 H H9 N N N 0 -3.015 2.017 0.074
27 H10 H H10 N N N 0 -2.684 0.917 1.433
28 H11 H H11 N N N 0 -0.938 1.257 -1.047
29 H12 H H12 N N N 0 -0.927 -3.513 -0.472
30 H13 H H13 N N N 0 0.614 -2.674 -0.169
31 H14 H H14 N N N 0 -0.576 -2.852 1.143
32 H15 H H15 N N N 0 -4.847 -0.26 1.008
33 H16 H H16 N N N 0 -5.178 0.84 -0.352
34 H17 H H17 N N N 0 -5.197 -0.922 -0.607
35 H18 H H18 N N N 0 -0.429 2.247 1.856
36 H19 H H19 N N N 0 0.672 3.998 0.658
37 H20 H H20 N N N 0 0.223 3.174 -0.96
38 H21 H H21 N N N 0 2.352 -0.658 2.994
39 H3 H H3 N N N 0 3.07 0.152 -2.431



F5F : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C15 C10 C C sing 1.53 N N
2 O9 C4 O C doub 1.22 N N
3 N3 C4 N C sing 1.35 N N
4 N3 C2 N C sing 1.36 N N
5 C10 C11 C C sing 1.53 N N
6 C10 C7 C C sing 1.53 N N
7 C4 C5 C C sing 1.4 N N
8 C2 C1 C C doub 1.35 N N
9 C11 C12 C C sing 1.53 N N
10 C5 C7 C C sing 1.51 N N
11 C5 C6 C C doub 1.38 N N
12 C1 C6 C C sing 1.41 N N
13 C12 C16 C C sing 1.53 N N
14 C12 C13 C C sing 1.53 N N
15 C7 C14 C C sing 1.53 N N
16 C6 O8 C O sing 1.35 N N
17 C14 C13 C C sing 1.53 N N
18 C14 C17 C C sing 1.51 N N
19 C17 C18 C C doub 1.31 N N
20 C1 H1 C H sing 1.08 N N
21 C2 H2 C H sing 1.08 N N
22 C7 H4 C H sing 1.09 N N
23 C10 H5 C H sing 1.09 N N
24 C11 H6 C H sing 1.09 N N
25 C11 H7 C H sing 1.09 N N
26 C12 H8 C H sing 1.09 N N
27 C13 H9 C H sing 1.09 N N
28 C13 H10 C H sing 1.09 N N
29 C14 H11 C H sing 1.09 N N
30 C15 H12 C H sing 1.09 N N
31 C15 H13 C H sing 1.09 N N
32 C15 H14 C H sing 1.09 N N
33 C16 H15 C H sing 1.09 N N
34 C16 H16 C H sing 1.09 N N
35 C16 H17 C H sing 1.09 N N
36 C17 H18 C H sing 1.08 N N
37 C18 H19 C H sing 1.08 N N
38 C18 H20 C H sing 1.08 N N
39 O8 H21 O H sing 0.97 N N
40 N3 H3 N H sing 0.97 N N



F5F : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
F5F 7bql Open in New Window Bound ligand 2 1