Chemical Components in the PDB

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Y10 : Summary

Code

Y10

One-letter code

X

Molecule name

(E,2R,3R,4S,5R)-N-(2,3-dihydro-1H-inden-2-yl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (2R,3R,4S,5R,6E)-N-(2,3-dihydro-1H-inden-2-yl)-3,4,5-trihydroxy-2-methoxy-8,8-dimethylnon-6-enamide (non-preferred name)
OpenEye OEToolkits 1.7.6 (E,2R,3R,4S,5R)-N-(2,3-dihydro-1H-inden-2-yl)-2-methoxy-8,8-dimethyl-3,4,5-tris(oxidanyl)non-6-enamide

Formula

C21 H31 N O5

Formal charge

0

Molecular weight

377.475 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(NC2Cc1ccccc1C2)C(OC)C(O)C(O)C(O)/C=C/C(C)(C)C
SMILES CACTVS 3.370 CO[CH]([CH](O)[CH](O)[CH](O)C=CC(C)(C)C)C(=O)NC1Cc2ccccc2C1
SMILES OpenEye OEToolkits 1.7.6 CC(C)(C)C=CC(C(C(C(C(=O)NC1Cc2ccccc2C1)OC)O)O)O
Canonical SMILES CACTVS 3.370 CO[C@H]([C@H](O)[C@@H](O)[C@H](O)/C=C/C(C)(C)C)C(=O)NC1Cc2ccccc2C1
Canonical SMILES OpenEye OEToolkits 1.7.6 CC(C)(C)/C=C/[C@H]([C@@H]([C@H]([C@H](C(=O)NC1Cc2ccccc2C1)OC)O)O)O

IUPAC InChI

InChI=1S/C21H31NO5/c1-21(2,3)10-9-16(23)17(24)18(25)19(27-4)20(26)22-15-11-13-7-5-6-8-14(13)12-15/h5-10,15-19,23-25H,11-12H2,1-4H3,(H,22,26)/b10-9+/t16-,17+,18-,19-/m1/s1

IUPAC InChI key

XTHOIFAGDPGJPZ-PQQJDVFMSA-N
Y10

wwPDB Information

Atom count

58 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-11-15

Last modified at

2012-06-17

Status

Released

Obsoleted

Not Assigned



Y10 : Atoms of Molecule

Total Number of Atoms: 58
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N N N N 0 -2.061 -0.856 -0.498
2 O1 O O1 N N N 0 2.354 1.536 0.631
3 O2 O O2 N N N 0 0.248 0.413 0.088
4 O3 O O3 N N N 0 2.524 -0.744 -1.11
5 O4 O O4 N N N 0 -1.973 -2.745 0.663
6 O5 O O5 N N N 0 0.578 -3.221 0.404
7 C01 C C01 N N N 0 6.42 1.473 -0.211
8 C02 C C02 N N N 0 4.959 1.437 0.157
9 C03 C C03 N N N 0 4.434 0.343 0.651
10 C04 C C04 R N N 0 2.973 0.307 1.019
11 C05 C C05 S N N 0 2.293 -0.857 0.295
12 C06 C C06 R N N 0 0.789 -0.819 0.569
13 C07 C C07 R N N 0 0.11 -1.988 -0.147
14 C08 C C08 N N N 0 7.055 0.114 0.089
15 C09 C C09 N N N 0 6.563 1.784 -1.702
16 C10 C C10 N N N 0 7.125 2.557 0.606
17 C11 C C11 N N N 0 -1.383 -1.891 0.036
18 C12 C C12 N N N 0 -3.511 -0.759 -0.315
19 C13 C C13 N N N 0 -4.153 0.067 -1.45
20 C14 C C14 N Y N 0 -5.286 0.828 -0.795
21 C15 C C15 N Y N 0 -5.112 0.835 0.576
22 C16 C C16 N N N 0 -3.852 0.078 0.937
23 C17 C C17 N Y N 0 -6.381 1.464 -1.354
24 C18 C C18 N Y N 0 -7.3 2.105 -0.546
25 C19 C C19 N Y N 0 -7.127 2.112 0.825
26 C20 C C20 N Y N 0 -6.035 1.478 1.385
27 C21 C C21 N N N 0 1.472 -3.938 -0.451
28 HN H HN N N N 0 -1.588 -0.174 -0.999
29 HO1 H HO1 N N N 0 2.405 1.72 -0.317
30 HO2 H HO2 N N N 0 0.368 0.551 -0.861
31 HO3 H HO3 N N N 0 2.184 0.072 -1.501
32 H02 H H02 N N N 0 4.344 2.313 0.013
33 H03 H H03 N N N 0 5.049 -0.533 0.795
34 H04 H H04 N N N 0 2.873 0.174 2.096
35 H05 H H05 N N N 0 2.705 -1.799 0.657
36 H06 H H06 N N N 0 0.613 -0.899 1.642
37 H07 H H07 N N N 0 0.349 -1.951 -1.21
38 H08 H H08 N N N 0 6.552 -0.659 -0.493
39 H08A H H08A N N N 0 8.111 0.14 -0.177
40 H08B H H08B N N N 0 6.953 -0.108 1.152
41 H09 H H09 N N N 0 6.06 1.012 -2.284
42 H09A H H09A N N N 0 6.11 2.753 -1.916
43 H09B H H09B N N N 0 7.619 1.81 -1.968
44 H10 H H10 N N N 0 8.182 2.583 0.34
45 H10A H H10A N N N 0 6.673 3.525 0.392
46 H10B H H10B N N N 0 7.023 2.335 1.669
47 H12 H H12 N N N 0 -3.96 -1.75 -0.256
48 H13 H H13 N N N 0 -3.425 0.761 -1.872
49 H13A H H13A N N N 0 -4.539 -0.593 -2.227
50 H16 H H16 N N N 0 -4.033 -0.575 1.79
51 H16A H H16A N N N 0 -3.043 0.775 1.157
52 H17 H H17 N N N 0 -6.517 1.46 -2.425
53 H18 H H18 N N N 0 -8.153 2.601 -0.986
54 H19 H H19 N N N 0 -7.844 2.612 1.458
55 H20 H H20 N N N 0 -5.9 1.483 2.456
56 H21 H H21 N N N 0 2.3 -3.289 -0.736
57 H21A H H21A N N N 0 1.857 -4.81 0.076
58 H21B H H21B N N N 0 0.938 -4.26 -1.345



Y10 : Chemical Bonds

Total Number of Bonds: 59
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C12 N C N sing 1.46 N N
2 N C11 N C sing 1.35 N N
3 N HN N H sing 0.97 N N
4 C04 O1 C O sing 1.43 N N
5 O1 HO1 O H sing 0.97 N N
6 C06 O2 C O sing 1.43 N N
7 O2 HO2 O H sing 0.97 N N
8 C05 O3 C O sing 1.43 N N
9 O3 HO3 O H sing 0.97 N N
10 O4 C11 O C doub 1.21 N N
11 C07 O5 C O sing 1.43 N N
12 O5 C21 O C sing 1.43 N N
13 C09 C01 C C sing 1.53 N N
14 C10 C01 C C sing 1.53 N N
15 C01 C08 C C sing 1.53 N N
16 C01 C02 C C sing 1.51 N N
17 C02 C03 C C doub 1.31 E N
18 C02 H02 C H sing 1.08 N N
19 C03 C04 C C sing 1.51 N N
20 C03 H03 C H sing 1.08 N N
21 C04 C05 C C sing 1.53 N N
22 C04 H04 C H sing 1.09 N N
23 C06 C05 C C sing 1.53 N N
24 C05 H05 C H sing 1.09 N N
25 C07 C06 C C sing 1.53 N N
26 C06 H06 C H sing 1.09 N N
27 C11 C07 C C sing 1.51 N N
28 C07 H07 C H sing 1.09 N N
29 C08 H08 C H sing 1.09 N N
30 C08 H08A C H sing 1.09 N N
31 C08 H08B C H sing 1.09 N N
32 C09 H09 C H sing 1.09 N N
33 C09 H09A C H sing 1.09 N N
34 C09 H09B C H sing 1.09 N N
35 C10 H10 C H sing 1.09 N N
36 C10 H10A C H sing 1.09 N N
37 C10 H10B C H sing 1.09 N N
38 C16 C12 C C sing 1.54 N N
39 C12 C13 C C sing 1.54 N N
40 C12 H12 C H sing 1.09 N N
41 C14 C13 C C sing 1.51 N N
42 C13 H13 C H sing 1.09 N N
43 C13 H13A C H sing 1.09 N N
44 C15 C14 C C doub 1.38 N Y
45 C17 C14 C C sing 1.38 N Y
46 C20 C15 C C sing 1.39 N Y
47 C15 C16 C C sing 1.51 N N
48 C16 H16 C H sing 1.09 N N
49 C16 H16A C H sing 1.09 N N
50 C18 C17 C C doub 1.38 N Y
51 C17 H17 C H sing 1.08 N N
52 C19 C18 C C sing 1.38 N Y
53 C18 H18 C H sing 1.08 N N
54 C19 C20 C C doub 1.38 N Y
55 C19 H19 C H sing 1.08 N N
56 C20 H20 C H sing 1.08 N N
57 C21 H21 C H sing 1.09 N N
58 C21 H21A C H sing 1.09 N N
59 C21 H21B C H sing 1.09 N N



Y10 : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
Y10 3pkd Open in New Window Bound ligand 1 1
Y10 3pke Open in New Window Bound ligand 1 1
Y10 4flk Open in New Window Bound ligand 1 1