Chemical Components in the PDB

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5YM : Summary

Code

5YM

One-letter code

X

Molecule name

(Z)-N-(2-hydroxyethyl)octadec-9-enamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (~{Z})-~{N}-(2-hydroxyethyl)octadec-9-enamide

Formula

C20 H39 N O2

Formal charge

0

Molecular weight

325.529 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCCCCCCCC=CCCCCCCCC(=O)NCCO
SMILES OpenEye OEToolkits 2.0.7 CCCCCCCCC=CCCCCCCCC(=O)NCCO
Canonical SMILES CACTVS 3.385 CCCCCCCC\C=C/CCCCCCCC(=O)NCCO
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCCCCCC/C=C\CCCCCCCC(=O)NCCO

IUPAC InChI

InChI=1S/C20H39NO2/c1-2-3-4-5-6-7-8-9-10-11-12-13-14-15-16-17-20(23)21-18-19-22/h9-10,22H,2-8,11-19H2,1H3,(H,21,23)/b10-9-

IUPAC InChI key

BOWVQLFMWHZBEF-KTKRTIGZSA-N
5YM

wwPDB Information

Atom count

62 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-08-25

Last modified at

2022-05-13

Status

Released

Obsoleted

Not Assigned



5YM : Atoms of Molecule

Total Number of Atoms: 62
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C13 C C1 N N N 0 -0.742 -1.259 0.549
2 C12 C C2 N N N 0 0.166 -2.428 0.159
3 C11 C C3 N N N 0 1.599 -2.132 0.607
4 C10 C C4 N N N 0 2.493 -3.283 0.223
5 C14 C C5 N N N 0 -2.174 -1.555 0.101
6 C15 C C6 N N N 0 -3.082 -0.387 0.491
7 C21 C C7 N N N 0 -9.185 0.807 -0.198
8 C16 C C8 N N N 0 -4.515 -0.682 0.043
9 C17 C C9 N N N 0 -5.423 0.486 0.434
10 C18 C C10 N N N 0 -6.834 0.195 -0.008
11 C22 C C11 N N N 0 -10.092 1.975 0.193
12 C01 C C12 N N N 0 11.23 3.295 0.405
13 C02 C C13 N N N 0 9.783 3.136 -0.065
14 C03 C C14 N N N 0 9.318 1.701 0.191
15 C04 C C15 N N N 0 7.871 1.542 -0.28
16 C05 C C16 N N N 0 7.407 0.106 -0.024
17 C06 C C17 N N N 0 5.959 -0.053 -0.494
18 C07 C C18 N N N 0 5.495 -1.488 -0.239
19 C08 C C19 N N N 0 4.048 -1.647 -0.709
20 C09 C C20 N N N 0 3.59 -3.06 -0.457
21 N20 N N1 N N N 0 -7.813 1.089 0.231
22 O19 O O1 N N N 0 -7.089 -0.845 -0.578
23 O23 O O2 N N N 0 -9.703 3.143 -0.532
24 H1 H H1 N N N 0 -0.719 -1.128 1.631
25 H2 H H2 N N N 0 -0.39 -0.348 0.065
26 H3 H H3 N N N 0 -0.186 -3.338 0.643
27 H4 H H4 N N N 0 0.144 -2.559 -0.923
28 H5 H H5 N N N 0 1.95 -1.221 0.123
29 H6 H H6 N N N 0 1.621 -2.0 1.689
30 H7 H H7 N N N 0 2.229 -4.29 0.508
31 H8 H H8 N N N 0 -2.197 -1.687 -0.981
32 H9 H H9 N N N 0 -2.526 -2.466 0.586
33 H10 H H10 N N N 0 -3.06 -0.255 1.573
34 H11 H H11 N N N 0 -2.731 0.524 0.007
35 H12 H H12 N N N 0 -9.536 -0.104 0.287
36 H13 H H13 N N N 0 -9.207 0.675 -1.28
37 H14 H H14 N N N 0 -4.537 -0.814 -1.038
38 H15 H H15 N N N 0 -4.867 -1.593 0.528
39 H16 H H16 N N N 0 -5.4 0.618 1.515
40 H17 H H17 N N N 0 -5.071 1.397 -0.051
41 H18 H H18 N N N 0 -11.127 1.727 -0.046
42 H19 H H19 N N N 0 -10.002 2.164 1.262
43 H20 H H20 N N N 0 11.869 2.603 -0.144
44 H21 H H21 N N N 0 11.561 4.317 0.223
45 H22 H H22 N N N 0 11.292 3.077 1.472
46 H23 H H23 N N N 0 9.144 3.828 0.485
47 H24 H H24 N N N 0 9.721 3.353 -1.131
48 H25 H H25 N N N 0 9.957 1.009 -0.359
49 H26 H H26 N N N 0 9.38 1.483 1.257
50 H27 H H27 N N N 0 7.233 2.233 0.27
51 H28 H H28 N N N 0 7.81 1.759 -1.346
52 H29 H H29 N N N 0 8.045 -0.585 -0.573
53 H30 H H30 N N N 0 7.468 -0.111 1.042
54 H31 H H31 N N N 0 5.321 0.639 0.055
55 H32 H H32 N N N 0 5.898 0.165 -1.561
56 H33 H H33 N N N 0 6.133 -2.18 -0.788
57 H34 H H34 N N N 0 5.556 -1.705 0.827
58 H35 H H35 N N N 0 3.409 -0.955 -0.16
59 H36 H H36 N N N 0 3.986 -1.429 -1.775
60 H37 H H37 N N N 0 4.167 -3.891 -0.838
61 H38 H H38 N N N 0 -7.609 1.921 0.688
62 H39 H H39 N N N 0 -10.237 3.925 -0.334



5YM : Chemical Bonds

Total Number of Bonds: 61
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C01 C02 C C sing 1.53 N N
2 C05 C06 C C sing 1.53 N N
3 C05 C04 C C sing 1.53 N N
4 C06 C07 C C sing 1.53 N N
5 C02 C03 C C sing 1.53 N N
6 C03 C04 C C sing 1.53 N N
7 C07 C08 C C sing 1.53 N N
8 C08 C09 C C sing 1.51 N N
9 C09 C10 C C doub 1.31 Z N
10 C11 C10 C C sing 1.51 N N
11 C11 C12 C C sing 1.53 N N
12 C12 C13 C C sing 1.53 N N
13 C13 C14 C C sing 1.53 N N
14 C14 C15 C C sing 1.53 N N
15 C15 C16 C C sing 1.53 N N
16 C17 C16 C C sing 1.53 N N
17 C17 C18 C C sing 1.51 N N
18 C18 N20 C N sing 1.35 N N
19 C18 O19 C O doub 1.21 N N
20 O23 C22 O C sing 1.43 N N
21 N20 C21 N C sing 1.46 N N
22 C22 C21 C C sing 1.53 N N
23 C13 H1 C H sing 1.09 N N
24 C13 H2 C H sing 1.09 N N
25 C12 H3 C H sing 1.09 N N
26 C12 H4 C H sing 1.09 N N
27 C11 H5 C H sing 1.09 N N
28 C11 H6 C H sing 1.09 N N
29 C10 H7 C H sing 1.08 N N
30 C14 H8 C H sing 1.09 N N
31 C14 H9 C H sing 1.09 N N
32 C15 H10 C H sing 1.09 N N
33 C15 H11 C H sing 1.09 N N
34 C21 H12 C H sing 1.09 N N
35 C21 H13 C H sing 1.09 N N
36 C16 H14 C H sing 1.09 N N
37 C16 H15 C H sing 1.09 N N
38 C17 H16 C H sing 1.09 N N
39 C17 H17 C H sing 1.09 N N
40 C22 H18 C H sing 1.09 N N
41 C22 H19 C H sing 1.09 N N
42 C01 H20 C H sing 1.09 N N
43 C01 H21 C H sing 1.09 N N
44 C01 H22 C H sing 1.09 N N
45 C02 H23 C H sing 1.09 N N
46 C02 H24 C H sing 1.09 N N
47 C03 H25 C H sing 1.09 N N
48 C03 H26 C H sing 1.09 N N
49 C04 H27 C H sing 1.09 N N
50 C04 H28 C H sing 1.09 N N
51 C05 H29 C H sing 1.09 N N
52 C05 H30 C H sing 1.09 N N
53 C06 H31 C H sing 1.09 N N
54 C06 H32 C H sing 1.09 N N
55 C07 H33 C H sing 1.09 N N
56 C07 H34 C H sing 1.09 N N
57 C08 H35 C H sing 1.09 N N
58 C08 H36 C H sing 1.09 N N
59 C09 H37 C H sing 1.08 N N
60 N20 H38 N H sing 0.97 N N
61 O23 H39 O H sing 0.97 N N



5YM : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
5YM 7v7w Open in New Window Bound ligand 1 1
5YM 8x2k Open in New Window Bound ligand 1 1