Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

6CM : Summary

Code

6CM

One-letter code

X

Molecule name

N-((E,2S,3R)-1,3-DIHYDROXYOCTADEC-4-EN-2-YL)HEXANAMIDE

Synonyms

C6-CERAMIDE
N-HEXANOYL-D-ERYTHRO-SPHINGOSINE
(2S,3R,4E)-2-HEXANOYLAMINOOCTADEC-4-ENE-1,3-DIOL
(2S,3R,4E)-2-HEXANOYLAMINO-1,3-OCTADEC-4-ENEDIOL

Systematic names

ProgramVersionName
ACDLabs 10.04 N-[(1S,2R,3E)-2-hydroxy-1-(hydroxymethyl)heptadec-3-en-1-yl]hexanamide
OpenEye OEToolkits 1.5.0 N-[(E,2S,3R)-1,3-dihydroxyoctadec-4-en-2-yl]hexanamide

Formula

C24 H47 N O3

Formal charge

0

Molecular weight

397.635 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(NC(CO)C(O)/C=C/CCCCCCCCCCCCC)CCCCC
SMILES CACTVS 3.341 CCCCCCCCCCCCCC=C[CH](O)[CH](CO)NC(=O)CCCCC
SMILES OpenEye OEToolkits 1.5.0 CCCCCCCCCCCCCC=CC(C(CO)NC(=O)CCCCC)O
Canonical SMILES CACTVS 3.341 CCCCCCCCCCCCC/C=C/[C@@H](O)[C@H](CO)NC(=O)CCCCC
Canonical SMILES OpenEye OEToolkits 1.5.0 CCCCCCCCCCCCC\C=C\[C@H]([C@H](CO)NC(=O)CCCCC)O

IUPAC InChI

InChI=1S/C24H47NO3/c1-3-5-7-8-9-10-11-12-13-14-15-16-18-19-23(27)22(21-26)25-24(28)20-17-6-4-2/h18-19,22-23,26-27H,3-17,20-21H2,1-2H3,(H,25,28)/b19-18+/t22-,23+/m0/s1

IUPAC InChI key

NPRJSFWNFTXXQC-QFWQFVLDSA-N
6CM

wwPDB Information

Atom count

75 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2005-11-28

Last modified at

2020-05-26

Status

Released

Obsoleted

Not Assigned



6CM : Atoms of Molecule

Total Number of Atoms: 75
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O19 O O19 N N N 0 -5.234 -0.885 -1.533
2 C19 C C19 N N N 0 -5.454 -0.709 -0.354
3 N2 N N2 N N N 0 -5.413 0.536 0.161
4 C2 C C2 S N N 0 -5.104 1.677 -0.705
5 C1 C C1 N N N 0 -6.384 2.159 -1.389
6 O1 O O1 N N N 0 -7.294 2.653 -0.404
7 C3 C C3 R N N 0 -4.517 2.811 0.137
8 C4 C C4 N N N 0 -3.287 2.32 0.855
9 C5 C C5 N N N 0 -2.15 2.956 0.717
10 C6 C C6 N N N 0 -0.919 2.464 1.434
11 C7 C C7 N N N 0 0.205 2.236 0.422
12 C8 C C8 N N N 0 1.454 1.737 1.15
13 C9 C C9 N N N 0 2.578 1.509 0.138
14 C10 C C10 N N N 0 3.828 1.009 0.866
15 C11 C C11 N N N 0 4.952 0.781 -0.146
16 C12 C C12 N N N 0 6.201 0.282 0.582
17 C13 C C13 N N N 0 7.325 0.054 -0.43
18 C14 C C14 N N N 0 8.574 -0.445 0.298
19 C15 C C15 N N N 0 9.698 -0.673 -0.714
20 C16 C C16 N N N 0 10.948 -1.173 0.014
21 C17 C C17 N N N 0 12.072 -1.401 -0.998
22 C18 C C18 N N N 0 13.321 -1.9 -0.27
23 O3 O O3 N N N 0 -4.167 3.904 -0.714
24 C20 C C20 N N N 0 -5.772 -1.882 0.537
25 C21 C C21 N N N 0 -5.754 -3.17 -0.29
26 C22 C C22 N N N 0 -6.077 -4.361 0.614
27 C23 C C23 N N N 0 -6.058 -5.648 -0.212
28 C24 C C24 N N N 0 -6.381 -6.84 0.692
29 HN2 H HN2 N N N 0 -5.589 0.677 1.104
30 H2 H H2 N N N 0 -4.38 1.373 -1.461
31 H11 H 1H1 N N N 0 -6.142 2.956 -2.092
32 H12 H 2H1 N N N 0 -6.845 1.329 -1.926
33 HO1 H HO1 N N N 0 -8.086 2.946 -0.877
34 H3 H H3 N N N 0 -5.256 3.142 0.867
35 H4 H H4 N N N 0 -3.342 1.443 1.483
36 H5 H H5 N N N 0 -2.094 3.832 0.088
37 H61 H 1H6 N N N 0 -1.145 1.527 1.943
38 H62 H 2H6 N N N 0 -0.604 3.208 2.166
39 H71 H 1H7 N N N 0 0.431 3.173 -0.087
40 H72 H 2H7 N N N 0 -0.111 1.492 -0.31
41 H81 H 1H8 N N N 0 1.228 0.8 1.659
42 H82 H 2H8 N N N 0 1.77 2.481 1.882
43 H91 H 1H9 N N N 0 2.804 2.446 -0.371
44 H92 H 2H9 N N N 0 2.263 0.765 -0.594
45 H101 H 1H10 N N N 0 3.601 0.072 1.375
46 H102 H 2H10 N N N 0 4.143 1.753 1.598
47 H111 H 1H11 N N N 0 5.178 1.718 -0.655
48 H112 H 2H11 N N N 0 4.636 0.037 -0.878
49 H121 H 1H12 N N N 0 5.975 -0.655 1.091
50 H122 H 2H12 N N N 0 6.516 1.026 1.314
51 H131 H 1H13 N N N 0 7.551 0.991 -0.939
52 H132 H 2H13 N N N 0 7.009 -0.69 -1.162
53 H141 H 1H14 N N N 0 8.348 -1.382 0.807
54 H142 H 2H14 N N N 0 8.89 0.299 1.03
55 H151 H 1H15 N N N 0 9.924 0.263 -1.223
56 H152 H 2H15 N N N 0 9.383 -1.417 -1.446
57 H161 H 1H16 N N N 0 10.721 -2.11 0.523
58 H162 H 2H16 N N N 0 11.263 -0.429 0.746
59 H171 H 1H17 N N N 0 12.298 -0.464 -1.507
60 H172 H 2H17 N N N 0 11.756 -2.145 -1.73
61 H181 H 1H18 N N N 0 13.636 -1.156 0.462
62 H182 H 2H18 N N N 0 13.095 -2.837 0.239
63 H183 H 3H18 N N N 0 14.122 -2.063 -0.991
64 HO3 H HO3 N N N 0 -3.585 3.549 -1.4
65 H201 H 1H20 N N N 0 -5.027 -1.949 1.33
66 H202 H 2H20 N N N 0 -6.76 -1.747 0.977
67 H211 H 1H21 N N N 0 -6.499 -3.103 -1.083
68 H212 H 2H21 N N N 0 -4.766 -3.305 -0.73
69 H221 H 1H22 N N N 0 -5.332 -4.428 1.407
70 H222 H 2H22 N N N 0 -7.065 -4.226 1.054
71 H231 H 1H23 N N N 0 -6.803 -5.581 -1.005
72 H232 H 2H23 N N N 0 -5.07 -5.783 -0.652
73 H241 H 1H24 N N N 0 -5.637 -6.906 1.485
74 H242 H 2H24 N N N 0 -7.369 -6.704 1.132
75 H243 H 3H24 N N N 0 -6.368 -7.757 0.103



6CM : Chemical Bonds

Total Number of Bonds: 74
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O19 C19 O C doub 1.21 N N
2 C19 N2 C N sing 1.35 N N
3 C19 C20 C C sing 1.51 N N
4 N2 C2 N C sing 1.47 N N
5 N2 HN2 N H sing 0.97 N N
6 C2 C1 C C sing 1.53 N N
7 C2 C3 C C sing 1.53 N N
8 C2 H2 C H sing 1.09 N N
9 C1 O1 C O sing 1.43 N N
10 C1 H11 C H sing 1.09 N N
11 C1 H12 C H sing 1.09 N N
12 O1 HO1 O H sing 0.97 N N
13 C3 C4 C C sing 1.51 N N
14 C3 O3 C O sing 1.43 N N
15 C3 H3 C H sing 1.09 N N
16 C4 C5 C C doub 1.31 E N
17 C4 H4 C H sing 1.08 N N
18 C5 C6 C C sing 1.51 N N
19 C5 H5 C H sing 1.08 N N
20 C6 C7 C C sing 1.53 N N
21 C6 H61 C H sing 1.09 N N
22 C6 H62 C H sing 1.09 N N
23 C7 C8 C C sing 1.53 N N
24 C7 H71 C H sing 1.09 N N
25 C7 H72 C H sing 1.09 N N
26 C8 C9 C C sing 1.53 N N
27 C8 H81 C H sing 1.09 N N
28 C8 H82 C H sing 1.09 N N
29 C9 C10 C C sing 1.53 N N
30 C9 H91 C H sing 1.09 N N
31 C9 H92 C H sing 1.09 N N
32 C10 C11 C C sing 1.53 N N
33 C10 H101 C H sing 1.09 N N
34 C10 H102 C H sing 1.09 N N
35 C11 C12 C C sing 1.53 N N
36 C11 H111 C H sing 1.09 N N
37 C11 H112 C H sing 1.09 N N
38 C12 C13 C C sing 1.53 N N
39 C12 H121 C H sing 1.09 N N
40 C12 H122 C H sing 1.09 N N
41 C13 C14 C C sing 1.53 N N
42 C13 H131 C H sing 1.09 N N
43 C13 H132 C H sing 1.09 N N
44 C14 C15 C C sing 1.53 N N
45 C14 H141 C H sing 1.09 N N
46 C14 H142 C H sing 1.09 N N
47 C15 C16 C C sing 1.53 N N
48 C15 H151 C H sing 1.09 N N
49 C15 H152 C H sing 1.09 N N
50 C16 C17 C C sing 1.53 N N
51 C16 H161 C H sing 1.09 N N
52 C16 H162 C H sing 1.09 N N
53 C17 C18 C C sing 1.53 N N
54 C17 H171 C H sing 1.09 N N
55 C17 H172 C H sing 1.09 N N
56 C18 H181 C H sing 1.09 N N
57 C18 H182 C H sing 1.09 N N
58 C18 H183 C H sing 1.09 N N
59 O3 HO3 O H sing 0.97 N N
60 C20 C21 C C sing 1.53 N N
61 C20 H201 C H sing 1.09 N N
62 C20 H202 C H sing 1.09 N N
63 C21 C22 C C sing 1.53 N N
64 C21 H211 C H sing 1.09 N N
65 C21 H212 C H sing 1.09 N N
66 C22 C23 C C sing 1.53 N N
67 C22 H221 C H sing 1.09 N N
68 C22 H222 C H sing 1.09 N N
69 C23 C24 C C sing 1.53 N N
70 C23 H231 C H sing 1.09 N N
71 C23 H232 C H sing 1.09 N N
72 C24 H241 C H sing 1.09 N N
73 C24 H242 C H sing 1.09 N N
74 C24 H243 C H sing 1.09 N N



6CM : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
6CM 2e3n Open in New Window Bound ligand 1 1