Chemical Components in the PDB

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HMY : Summary

Code

HMY

One-letter code

X

Molecule name

(1aR,8S,13S,14S,15aR)-5,13,14-trihydroxy-3-methoxy-8-methyl-8,9,13,14,15,15a-hexahydro-6H-oxireno[k][2]benzoxacyclotetradecine-6,12(1aH)-dione

Systematic names

ProgramVersionName
ACDLabs 10.04 (1aR,8S,10Z,13S,14S,15aR)-5,13,14-trihydroxy-3-methoxy-8-methyl-8,9,13,14,15,15a-hexahydro-6H-oxireno[k][2]benzoxacyclotetradecine-6,12(1aH)-dione

Formula

C19 H22 O8

Formal charge

0

Molecular weight

378.373 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C3C=CCC(OC(=O)c1c(cc(OC)cc1O)C2OC2CC(O)C3O)C
SMILES CACTVS 3.341 COc1cc(O)c2C(=O)O[CH](C)CC=CC(=O)[CH](O)[CH](O)C[CH]3O[CH]3c2c1
SMILES OpenEye OEToolkits 1.5.0 CC1CC=CC(=O)C(C(CC2C(O2)c3cc(cc(c3C(=O)O1)O)OC)O)O
Canonical SMILES CACTVS 3.341 COc1cc(O)c2C(=O)O[C@@H](C)C\C=C/C(=O)[C@@H](O)[C@@H](O)C[C@H]3O[C@@H]3c2c1
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@H]1CC=CC(=O)[C@H]([C@H](C[C@@H]2[C@H](O2)c3cc(cc(c3C(=O)O1)O)OC)O)O

IUPAC InChI

InChI=1S/C19H22O8/c1-9-4-3-5-12(20)17(23)14(22)8-15-18(27-15)11-6-10(25-2)7-13(21)16(11)19(24)26-9/h3,5-7,9,14-15,17-18,21-23H,4,8H2,1-2H3/t9-,14-,15+,17+,18+/m0/s1

IUPAC InChI key

SSNQAUBBJYCSMY-LWQPPDATSA-N
HMY

wwPDB Information

Atom count

49 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-02-19

Last modified at

2024-09-27

Status

Released

Obsoleted

Not Assigned



HMY : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O23 O O23 N N N 0 0.551 0.446 0.962
2 C7 C C7 N N N 0 -0.294 1.147 0.45
3 O8 O O8 N N N 0 -0.031 2.397 0.048
4 C9 C C9 S N N 0 1.301 2.945 0.065
5 C25 C C25 N N N 0 1.908 2.892 1.466
6 C10 C C10 N N N 0 2.194 2.217 -0.941
7 C11 C C11 N N N 0 3.601 2.143 -0.438
8 C12 C C12 N N N 0 4.318 1.06 -0.225
9 C2 C C2 N Y N 0 -1.648 0.593 0.252
10 C1 C C1 N Y N 0 -2.697 1.456 -0.111
11 O20 O O20 N N N 0 -2.471 2.781 -0.293
12 C6 C C6 N Y N 0 -3.977 0.954 -0.282
13 C5 C C5 N Y N 0 -4.215 -0.4 -0.099
14 O21 O O21 N N N 0 -5.469 -0.892 -0.257
15 C22 C C22 N N N 0 -6.493 0.04 -0.612
16 C4 C C4 N Y N 0 -3.171 -1.251 0.241
17 C3 C C3 N Y N 0 -1.898 -0.769 0.407
18 C18 C C18 R N N 0 -0.813 -1.766 0.746
19 O31 O O31 N N N 0 -1.088 -3.091 0.254
20 C17 C C17 R N N 0 0.018 -2.397 -0.354
21 C16 C C16 N N N 0 1.373 -3.045 -0.078
22 C15 C C15 S N N 0 2.41 -2.056 0.428
23 O29 O O29 N N N 0 2.026 -1.534 1.7
24 C14 C C14 S N N 0 2.612 -0.91 -0.567
25 O28 O O28 N N N 0 2.487 -1.413 -1.9
26 C13 C C13 N N N 0 3.984 -0.336 -0.386
27 O24 O O24 N N N 0 4.917 -1.134 -0.374
28 H9 H H9 N N N 0 1.245 4.004 -0.239
29 H25 H H25 N N N 0 1.955 1.856 1.803
30 H25A H H25A N N N 0 2.912 3.313 1.443
31 H25B H H25B N N N 0 1.287 3.469 2.152
32 H12 H H12 N N N 0 5.35 1.26 0.138
33 H10 H H10 N N N 0 1.792 1.244 -1.177
34 H10A H H10A N N N 0 2.194 2.805 -1.875
35 H11 H H11 N N N 0 4.105 3.104 -0.234
36 HO20 H HO20 N N N 0 -2.231 3.018 -1.199
37 H6 H H6 N N N 0 -4.785 1.615 -0.556
38 H22 H H22 N N N 0 -7.444 -0.484 -0.706
39 H22A H H22A N N N 0 -6.573 0.803 0.163
40 H22B H H22B N N N 0 -6.242 0.512 -1.561
41 H4 H H4 N N N 0 -3.361 -2.305 0.382
42 H18 H H18 N N N 0 -0.405 -1.692 1.752
43 H17 H H17 N N N 0 -0.133 -2.049 -1.381
44 H16 H H16 N N N 0 1.237 -3.836 0.67
45 H16A H H16A N N N 0 1.736 -3.519 -0.996
46 H15 H H15 N N N 0 3.369 -2.579 0.549
47 HO29 H HO29 N N N 0 2.653 -0.897 2.07
48 H14 H H14 N N N 0 1.854 -0.158 -0.389
49 HO28 H HO28 N N N 0 2.603 -0.742 -2.587



HMY : Chemical Bonds

Total Number of Bonds: 51
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O23 C7 O C doub 1.21 N N
2 C7 O8 C O sing 1.34 N N
3 C7 C2 C C sing 1.48 N N
4 O8 C9 O C sing 1.44 N N
5 C9 C25 C C sing 1.53 N N
6 C9 C10 C C sing 1.53 N N
7 C10 C11 C C sing 1.5 N N
8 C11 C12 C C doub 1.32 N N
9 C12 C13 C C sing 1.44 N N
10 C2 C1 C C doub 1.41 N Y
11 C2 C3 C C sing 1.39 N Y
12 C1 O20 C O sing 1.36 N N
13 C1 C6 C C sing 1.39 N Y
14 C6 C5 C C doub 1.39 Z Y
15 C5 O21 C O sing 1.36 N N
16 C5 C4 C C sing 1.39 N Y
17 O21 C22 O C sing 1.43 N N
18 C4 C3 C C doub 1.37 N Y
19 C3 C18 C C sing 1.51 N N
20 C18 O31 C O sing 1.44 N N
21 C18 C17 C C sing 1.52 N N
22 O31 C17 O C sing 1.44 N N
23 C17 C16 C C sing 1.53 N N
24 C16 C15 C C sing 1.52 N N
25 C15 O29 C O sing 1.43 N N
26 C15 C14 C C sing 1.53 N N
27 C14 O28 C O sing 1.43 N N
28 C14 C13 C C sing 1.5 N N
29 C13 O24 C O doub 1.23 N N
30 C9 H9 C H sing 1.1 N N
31 C25 H25 C H sing 1.09 N N
32 C25 H25A C H sing 1.09 N N
33 C25 H25B C H sing 1.09 N N
34 C10 H10 C H sing 1.08 N N
35 C10 H10A C H sing 1.1 N N
36 C11 H11 C H sing 1.1 N N
37 C12 H12 C H sing 1.11 N N
38 O20 HO20 O H sing 0.97 N N
39 C6 H6 C H sing 1.08 N N
40 C22 H22 C H sing 1.09 N N
41 C22 H22A C H sing 1.09 N N
42 C22 H22B C H sing 1.09 N N
43 C4 H4 C H sing 1.08 N N
44 C18 H18 C H sing 1.09 N N
45 C17 H17 C H sing 1.09 N N
46 C16 H16 C H sing 1.1 N N
47 C16 H16A C H sing 1.1 N N
48 C15 H15 C H sing 1.1 N N
49 O29 HO29 O H sing 0.97 N N
50 C14 H14 C H sing 1.08 N N
51 O28 HO28 O H sing 0.97 N N



HMY : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
HMY 3c9w Open in New Window Bound ligand 2 1