Chemical Components in the PDB

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18Y : Summary

Code

18Y

One-letter code

X

Molecule name

Trioxacarcin A analogue, bound form

Synonyms

(1S,2R,3aS,4S,13aS)-2-(dimethoxymethyl)-1,12-dihydroxy-7-methoxy-1,5-dimethyl-11-oxo-1,2,3a,4,8,9,10,11-octahydro-13aH-2,4-epoxyfuro[3,2-b]naphtho[2,3-h]chromen-13a-yl 4-C-acetyl-2,6-dideoxy-alpha-L-xylo-hexopyranoside

Systematic names

ProgramVersionName
ACDLabs 12.01 (1S,2R,3aS,4S,13aS)-2-(dimethoxymethyl)-1,12-dihydroxy-7-methoxy-1,5-dimethyl-11-oxo-1,2,3a,4,8,9,10,11-octahydro-13aH-2,4-epoxyfuro[3,2-b]naphtho[2,3-h]chromen-13a-yl 4-C-acetyl-2,6-dideoxy-alpha-L-xylo-hexopyranoside

Formula

C33 H40 O14

Formal charge

0

Molecular weight

660.662 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(C)C1(O)C(O)CC(OC1C)OC57Oc2c(c(cc4c2c(O)c3C(=O)CCCc3c4OC)C)C6OC(OC56)(C(OC)OC)C7(O)C
SMILES CACTVS 3.370 COC(OC)[C]12O[CH]3[CH](O1)[C](O[CH]4C[CH](O)[C](O)([CH](C)O4)C(C)=O)(Oc5c3c(C)cc6c(OC)c7CCCC(=O)c7c(O)c56)[C]2(C)O
SMILES OpenEye OEToolkits 1.7.6 Cc1cc2c(c(c3c(c2OC)CCCC3=O)O)c4c1C5C6C(O4)(C(C(O5)(O6)C(OC)OC)(C)O)OC7CC(C(C(O7)C)(C(=O)C)O)O
Canonical SMILES CACTVS 3.370 COC(OC)[C@]12O[C@@H]3[C@H](O1)[C@@](O[C@H]4C[C@@H](O)[C@](O)([C@H](C)O4)C(C)=O)(Oc5c3c(C)cc6c(OC)c7CCCC(=O)c7c(O)c56)[C@]2(C)O
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1cc2c(c(c3c(c2OC)CCCC3=O)O)c4c1[C@H]5[C@H]6[C@@](O4)([C@]([C@@](O5)(O6)C(OC)OC)(C)O)O[C@H]7C[C@H]([C@]([C@@H](O7)C)(C(=O)C)O)O

IUPAC InChI

InChI=1S/C33H40O14/c1-13-11-17-23(24(37)22-16(25(17)40-5)9-8-10-18(22)35)26-21(13)27-28-32(45-26,30(4,38)33(46-27,47-28)29(41-6)42-7)44-20-12-19(36)31(39,14(2)34)15(3)43-20/h11,15,19-20,27-29,36-39H,8-10,12H2,1-7H3/t15-,19+,20-,27-,28-,30-,31+,32+,33-/m0/s1

IUPAC InChI key

VSONDVKNAFWAKH-UEXNXLFMSA-N
18Y

wwPDB Information

Atom count

87 (47 without Hydrogen)

Polymer type

Saccharide

Type description

L-SACCHARIDE

Type code

ATOMS

Is modified

No

Standard parent

Not Assigned

Defined at

2012-11-08

Last modified at

2013-10-18

Status

Released

Obsoleted

Not Assigned



18Y : Atoms of Molecule

Total Number of Atoms: 87
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 -4.416 -2.448 -1.84
2 C1' C C1' S N N 0 2.083 -1.574 -0.507
3 C11 C C11 S N N 0 0.539 1.953 1.527
4 C12 C C12 S N N 0 1.605 1.022 0.9
5 C13 C C13 S N N 0 1.095 0.609 -0.506
6 C14 C C14 S N N 0 1.06 1.962 -1.257
7 C15 C C15 R N N 0 1.686 2.936 -0.212
8 C17 C C17 N N N 0 -0.378 2.366 -1.584
9 C18 C C18 N N N 0 -1.505 2.822 3.315
10 C19 C C19 N Y N 0 -4.757 -0.116 1.069
11 C2 C C2 N N N 0 -5.758 -3.141 -1.748
12 C2' C C2' N N N 0 3.013 -2.483 -1.316
13 C20 C C20 N Y N 0 -4.077 -1.472 -0.795
14 C21 C C21 N Y N 0 -5.068 -1.027 0.104
15 C22 C C22 N Y N 0 -2.44 -0.052 0.287
16 C23 C C23 N Y N 0 -3.444 0.391 1.18
17 C24 C C24 N N N 0 -6.475 1.459 1.543
18 C25 C C25 N N N 0 2.331 4.197 -0.79
19 C27 C C27 N N N 0 1.88 5.96 -2.35
20 C28 C C28 N N N 0 3.848 5.944 -0.163
21 C3 C C3 N N N 0 -6.798 -2.08 -1.365
22 C3' C C3' R N N 0 3.118 -3.843 -0.62
23 C4 C C4 N N N 0 -6.482 -1.542 0.028
24 C4' C C4' S N N 0 3.614 -3.633 0.815
25 C5 C C5 N Y N 0 -3.113 1.331 2.166
26 C5' C C5' S N N 0 2.66 -2.681 1.541
27 C6 C C6 N Y N 0 -1.841 1.808 2.252
28 C6' C C6' N N N 0 1.269 -3.312 1.618
29 C7 C C7 N Y N 0 -0.84 1.38 1.378
30 C7' C C7' N N N 0 4.998 -3.039 0.788
31 C8 C C8 N Y N 0 -1.127 0.453 0.402
32 C8' C C8' N N N 0 6.203 -3.939 0.687
33 C9 C C9 N Y N 0 -2.767 -0.993 -0.707
34 H1 H H1 N N N 0 1.868 2.73 -2.947
35 H1' H H1' N N N 0 1.084 -2.01 -0.479
36 H11 H H11 N N N 0 0.762 2.13 2.579
37 H111 H H111 N N N 0 -7.207 1.69 2.318
38 H112 H H112 N N N 0 -5.805 2.307 1.411
39 H113 H H113 N N N 0 -6.992 1.254 0.605
40 H12 H H12 N N N 0 1.954 0.207 1.534
41 H16 H H16 N N N 0 3.119 3.915 -1.489
42 H171 H H171 N N N 0 -0.948 2.463 -0.66
43 H172 H H172 N N N 0 -0.376 3.32 -2.112
44 H2 H H2 N N N 0 4.002 -2.028 -1.378
45 H2' H H2' N N N 0 2.609 -2.617 -2.319
46 H2A H H2A N N N 0 -6.015 -3.58 -2.712
47 H2B H H2B N N N 0 -5.723 -3.918 -0.984
48 H3 H H3 N N N 0 -0.836 1.603 -2.215
49 H3' H H3' N N N 0 2.138 -4.32 -0.602
50 H3A H H3A N N N 0 -6.768 -1.264 -2.086
51 H3B H H3B N N N 0 -7.792 -2.529 -1.364
52 H4' H H4' N N N 0 3.949 -4.83 2.413
53 H4A H H4A N N N 0 -7.171 -0.73 0.262
54 H4B H H4B N N N 0 -6.611 -2.34 0.758
55 H5 H H5 N N N 0 -3.868 1.678 2.858
56 H5' H H5' N N N 0 3.031 -2.494 2.549
57 H61' H H61' N N N 0 0.898 -3.499 0.61
58 H61A H H61A N N N 0 -1.184 2.306 4.22
59 H61B H H61B N N N 0 2.74 5.55 -2.879
60 H61C H H61C N N N 0 4.58 5.466 -0.813
61 H62' H H62' N N N 0 1.327 -4.253 2.165
62 H62A H H62A N N N 0 -2.387 3.424 3.534
63 H62B H H62B N N N 0 1.119 6.261 -3.07
64 H62C H H62C N N N 0 3.339 6.738 -0.71
65 H63' H H63' N N N 0 0.59 -2.633 2.135
66 H63A H H63A N N N 0 -0.703 3.468 2.96
67 H63B H H63B N N N 0 2.191 6.827 -1.768
68 H63C H H63C N N N 0 4.354 6.368 0.705
69 H81' H H81' N N N 0 7.109 -3.333 0.681
70 H82' H H82' N N N 0 6.223 -4.615 1.541
71 H83' H H83' N N N 0 6.147 -4.518 -0.235
72 H9 H H9 N N N 0 -1.342 -2.213 -1.27
73 HO3 H HO3 N N N 0 3.793 -4.841 -2.247
74 O1 O O1 N N N 0 -3.645 -2.69 -2.745
75 O1' O O1' N N N 0 2.585 -1.446 0.825
76 O10 O O10 N N N 0 -5.719 0.31 1.931
77 O11 O O11 N N N 0 0.64 3.175 0.766
78 O12 O O12 N N N 0 2.598 2.045 0.516
79 O13 O O13 N N N 0 2.025 -0.285 -1.12
80 O14 O O14 N N N 0 1.857 1.906 -2.441
81 O16 O O16 N N N 0 2.891 4.975 0.27
82 O26 O O26 N N N 0 1.341 4.967 -1.475
83 O3' O O3' N N N 0 4.042 -4.673 -1.328
84 O4' O O4' N N N 0 3.646 -4.889 1.497
85 O7' O O7' N N N 0 5.142 -1.841 0.847
86 O8 O O8 N N N 0 -0.177 0.014 -0.449
87 O9 O O9 N N N 0 -1.821 -1.43 -1.573



18Y : Chemical Bonds

Total Number of Bonds: 93
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C3 C4 C C sing 1.53 N N
2 C3 C2 C C sing 1.53 N N
3 C4 C21 C C sing 1.51 N N
4 C2 C1 C C sing 1.51 N N
5 O10 C19 O C sing 1.36 N N
6 O10 C24 O C sing 1.43 N N
7 C21 C19 C C doub 1.36 N Y
8 C21 C20 C C sing 1.41 N Y
9 C19 C23 C C sing 1.41 N Y
10 C1 C20 C C sing 1.47 N N
11 C1 O1 C O doub 1.21 N N
12 C20 C9 C C doub 1.4 N Y
13 C23 C5 C C doub 1.4 N Y
14 C23 C22 C C sing 1.41 N Y
15 C5 C6 C C sing 1.36 N Y
16 C9 C22 C C sing 1.41 N Y
17 C9 O9 C O sing 1.35 N N
18 C6' C5' C C sing 1.53 N N
19 C22 C8 C C doub 1.41 N Y
20 O4' C4' O C sing 1.43 N N
21 C6 C18 C C sing 1.51 N N
22 C6 C7 C C doub 1.4 N Y
23 O1' C5' O C sing 1.43 N N
24 O1' C1' O C sing 1.43 N N
25 C8 C7 C C sing 1.38 N Y
26 C8 O8 C O sing 1.35 N N
27 C5' C4' C C sing 1.53 N N
28 C7 C11 C C sing 1.5 N N
29 C4' C7' C C sing 1.51 N N
30 C4' C3' C C sing 1.53 N N
31 C1' C2' C C sing 1.53 N N
32 C1' O13 C O sing 1.43 N N
33 O8 C13 O C sing 1.41 N N
34 C8' C7' C C sing 1.51 N N
35 C11 C12 C C sing 1.55 N N
36 C11 O11 C O sing 1.44 N N
37 C2' C3' C C sing 1.53 N N
38 C7' O7' C O doub 1.21 N N
39 C12 C13 C C sing 1.55 N N
40 C12 O12 C O sing 1.48 N N
41 C3' O3' C O sing 1.43 N N
42 C13 O13 C O sing 1.43 N N
43 C13 C14 C C sing 1.55 N N
44 O12 C15 O C sing 1.47 N N
45 O11 C15 O C sing 1.45 N N
46 C14 C15 C C sing 1.56 N N
47 C14 C17 C C sing 1.53 N N
48 C14 O14 C O sing 1.43 N N
49 C15 C25 C C sing 1.53 N N
50 C25 O16 C O sing 1.43 N N
51 C25 O26 C O sing 1.43 N N
52 C28 O16 C O sing 1.43 N N
53 O26 C27 O C sing 1.43 N N
54 C3 H3A C H sing 1.09 N N
55 C3 H3B C H sing 1.09 N N
56 C5 H5 C H sing 1.08 N N
57 C8' H81' C H sing 1.09 N N
58 C8' H82' C H sing 1.09 N N
59 C8' H83' C H sing 1.09 N N
60 C2 H2B C H sing 1.09 N N
61 C2 H2A C H sing 1.09 N N
62 C4 H4A C H sing 1.09 N N
63 C4 H4B C H sing 1.09 N N
64 O9 H9 O H sing 0.97 N N
65 C11 H11 C H sing 1.09 N N
66 C12 H12 C H sing 1.09 N N
67 O14 H1 O H sing 0.97 N N
68 C25 H16 C H sing 1.09 N N
69 C1' H1' C H sing 1.09 N N
70 C2' H2' C H sing 1.09 N N
71 C2' H2 C H sing 1.09 N N
72 O3' HO3 O H sing 0.97 N N
73 C3' H3' C H sing 1.09 N N
74 O4' H4' O H sing 0.97 N N
75 C5' H5' C H sing 1.09 N N
76 C6' H61' C H sing 1.09 N N
77 C6' H62' C H sing 1.09 N N
78 C6' H63' C H sing 1.09 N N
79 C18 H61A C H sing 1.09 N N
80 C18 H63A C H sing 1.09 N N
81 C18 H62A C H sing 1.09 N N
82 C24 H111 C H sing 1.09 N N
83 C24 H112 C H sing 1.09 N N
84 C24 H113 C H sing 1.09 N N
85 C27 H62B C H sing 1.09 N N
86 C27 H63B C H sing 1.09 N N
87 C27 H61B C H sing 1.09 N N
88 C28 H63C C H sing 1.09 N N
89 C28 H61C C H sing 1.09 N N
90 C28 H62C C H sing 1.09 N N
91 C17 H171 C H sing 1.09 N N
92 C17 H172 C H sing 1.09 N N
93 C17 H3 C H sing 1.09 N N



18Y : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
18Y 4hp7 Open in New Window Bound ligand 4 1