Chemical Components in the PDB

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DM2 : Summary

Code

DM2

One-letter code

X

Molecule name

DOXORUBICIN

Synonyms

ADRIAMYCIN

Systematic names

ProgramVersionName
ACDLabs 10.04 (1S,3S)-3,5,12-trihydroxy-3-(hydroxyacetyl)-10-methoxy-6,11-dioxo-1,2,3,4,6,11-hexahydrotetracen-1-yl 3-amino-2,3,6-trideoxy-alpha-L-lyxo-hexopyranoside
OpenEye OEToolkits 1.5.0 (7S,9S)-7-[(2R,4S,5S,6S)-4-amino-5-hydroxy-6-methyl-oxan-2-yl]oxy-6,9,11-trihydroxy-9-(2-hydroxyethanoyl)-4-methoxy-8,10-dihydro-7H-tetracene-5,12-dione

Formula

C27 H29 N O11

Formal charge

0

Molecular weight

543.519 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C2c1c(O)c5c(c(O)c1C(=O)c3cccc(OC)c23)CC(O)(C(=O)CO)CC5OC4OC(C(O)C(N)C4)C
SMILES CACTVS 3.341 COc1cccc2C(=O)c3c(O)c4C[C](O)(C[CH](O[CH]5C[CH](N)[CH](O)[CH](C)O5)c4c(O)c3C(=O)c12)C(=O)CO
SMILES OpenEye OEToolkits 1.5.0 CC1C(C(CC(O1)OC2CC(Cc3c2c(c4c(c3O)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)CO)O)N)O
Canonical SMILES CACTVS 3.341 COc1cccc2C(=O)c3c(O)c4C[C@](O)(C[C@H](O[C@H]5C[C@H](N)[C@H](O)[C@H](C)O5)c4c(O)c3C(=O)c12)C(=O)CO
Canonical SMILES OpenEye OEToolkits 1.5.0 C[C@H]1[C@H]([C@H](C[C@@H](O1)O[C@H]2C[C@@](Cc3c2c(c4c(c3O)C(=O)c5cccc(c5C4=O)OC)O)(C(=O)CO)O)N)O

IUPAC InChI

InChI=1S/C27H29NO11/c1-10-22(31)13(28)6-17(38-10)39-15-8-27(36,16(30)9-29)7-12-19(15)26(35)21-20(24(12)33)23(32)11-4-3-5-14(37-2)18(11)25(21)34/h3-5,10,13,15,17,22,29,31,33,35-36H,6-9,28H2,1-2H3/t10-,13-,15-,17-,22+,27-/m0/s1

IUPAC InChI key

AOJJSUZBOXZQNB-TZSSRYMLSA-N
DM2

wwPDB Information

Atom count

68 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAD

Is modified

No

Standard parent

Not Assigned

Defined at

1999-07-08

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



DM2 : Atoms of Molecule

Total Number of Atoms: 68
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 -0.791 -0.376 6.114
2 C1' C C1* R N N 0 1.598 0.601 -2.737
3 C10 C C10 S N N 0 -0.413 -0.024 -1.829
4 C11 C C11 N N N 0 -1.412 -0.739 -2.736
5 C12 C C12 S N N 0 -2.828 -0.395 -2.259
6 C13 C C13 N N N 0 -2.962 1.096 -2.096
7 C14 C C14 N N N 0 -3.323 1.954 -3.282
8 C15 C C15 N N N 0 -3.061 -1.082 -0.915
9 C16 C C16 N Y N 0 -1.936 -0.777 0.039
10 C17 C C17 N Y N 0 -2.17 -1.005 1.402
11 C18 C C18 N Y N 0 -1.174 -0.751 2.341
12 C19 C C19 N N N 0 -1.41 -0.985 3.778
13 C2 C C2 N Y N 0 0.106 0.151 7.027
14 C2' C C2* N N N 0 3.094 0.283 -2.798
15 C20 C C20 N Y N 0 -0.462 -0.426 4.765
16 C21 C C21 N N N 0 3.562 1.529 6.029
17 C3 C C3 N Y N 0 1.331 0.63 6.611
18 C3' C C3* S N N 0 3.298 -1.006 -3.599
19 C4 C C4 N Y N 0 1.682 0.59 5.264
20 C4' C C4* S N N 0 2.607 -0.854 -4.959
21 C5 C C5 N Y N 0 0.784 0.066 4.332
22 C5' C C5* S N N 0 1.148 -0.45 -4.735
23 C6 C C6 N N N 0 1.136 0.0080 2.9
24 C6' C C6* N N N 0 0.441 -0.326 -6.086
25 C7 C C7 N Y N 0 0.076 -0.262 1.91
26 C8 C C8 N Y N 0 0.293 -0.04 0.553
27 C9 C C9 N Y N 0 -0.721 -0.297 -0.379
28 H1 H H1 N N N 0 -1.747 -0.749 6.45
29 H1' H H1* N N N 0 1.444 1.506 -2.149
30 H10 H H10 N N N 0 -0.466 1.048 -2.011
31 H111 H 1H11 N N N 0 -1.256 -1.816 -2.677
32 H112 H 2H11 N N N 0 -1.279 -0.403 -3.764
33 H141 H 1H14 N N N 0 -2.564 1.84 -4.057
34 H142 H 2H14 N N N 0 -4.291 1.643 -3.674
35 H151 H 1H15 N N N 0 -3.12 -2.16 -1.068
36 H152 H 2H15 N N N 0 -4.0 -0.729 -0.489
37 H2 H H2 N N N 0 -0.154 0.188 8.075
38 H2'1 H 1H2* N N N 0 3.621 1.103 -3.286
39 H2'2 H 2H2* N N N 0 3.48 0.15 -1.787
40 H211 H 1H21 N N N 0 4.541 1.92 5.752
41 H212 H 2H21 N N N 0 2.975 2.319 6.497
42 H213 H 3H21 N N N 0 3.686 0.704 6.731
43 H3 H H3 N N N 0 2.022 1.038 7.334
44 H3' H H3* N N N 0 2.86 -1.846 -3.059
45 H4' H H4* N N N 0 2.645 -1.802 -5.496
46 H5' H H5* N N N 0 0.65 -1.21 -4.134
47 H6'1 H 1H6* N N N 0 -0.597 -0.038 -5.927
48 H6'2 H 2H6* N N N 0 0.94 0.432 -6.689
49 H6'3 H 3H6* N N N 0 0.478 -1.284 -6.605
50 HN'1 H 1HN* N N N 0 5.144 -1.323 -2.877
51 HN'2 H 2HN* N N N 0 4.823 -2.147 -4.233
52 HO12 H 2HO1 N N N 0 -4.658 -0.643 -2.862
53 HO14 H 4HO1 N N N 0 -3.622 3.836 -3.663
54 HO17 H 7HO1 N N N 0 -3.932 -0.707 1.985
55 HO4' H *HO4 N N N 0 2.807 0.217 -6.568
56 HO8 H HO8 N N N 0 1.418 1.392 0.091
57 N3' N N3* N N N 0 4.735 -1.242 -3.796
58 O10 O O10 N N N 0 0.906 -0.487 -2.124
59 O12 O O12 N N N 0 -3.784 -0.864 -3.212
60 O13 O O13 N N N 0 -2.78 1.605 -1.016
61 O14 O O14 N N N 0 -3.389 3.323 -2.877
62 O17 O O17 N N N 0 -3.374 -1.478 1.809
63 O19 O O19 N N N 0 -2.373 -1.63 4.146
64 O4 O O4 N N N 0 2.887 1.062 4.859
65 O4' O O4* N N N 0 3.273 0.154 -5.723
66 O5' O O5* N N N 0 1.094 0.801 -4.056
67 O6 O O6 N N N 0 2.284 0.186 2.539
68 O8 O O8 N N N 0 1.493 0.428 0.131



DM2 : Chemical Bonds

Total Number of Bonds: 72
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C doub 1.38 N Y
2 C1 C20 C C sing 1.39 N Y
3 C1 H1 C H sing 1.08 N N
4 C2 C3 C C sing 1.38 N Y
5 C2 H2 C H sing 1.08 N N
6 C3 C4 C C doub 1.39 N Y
7 C3 H3 C H sing 1.08 N N
8 C4 O4 C O sing 1.36 N N
9 C4 C5 C C sing 1.4 N Y
10 O4 C21 O C sing 1.43 N N
11 C5 C6 C C sing 1.48 N N
12 C5 C20 C C doub 1.41 N Y
13 C6 O6 C O doub 1.22 N N
14 C6 C7 C C sing 1.48 N N
15 C7 C8 C C doub 1.39 N Y
16 C7 C18 C C sing 1.41 N Y
17 C8 O8 C O sing 1.36 N N
18 C8 C9 C C sing 1.4 N Y
19 O8 HO8 O H sing 0.97 N N
20 C9 C10 C C sing 1.51 N N
21 C9 C16 C C doub 1.37 N Y
22 C10 O10 C O sing 1.43 N N
23 C10 C11 C C sing 1.53 N N
24 C10 H10 C H sing 1.09 N N
25 O10 C1' O C sing 1.43 N N
26 C11 C12 C C sing 1.53 N N
27 C11 H111 C H sing 1.09 N N
28 C11 H112 C H sing 1.09 N N
29 C12 O12 C O sing 1.43 N N
30 C12 C13 C C sing 1.51 N N
31 C12 C15 C C sing 1.53 N N
32 O12 HO12 O H sing 0.97 N N
33 C13 O13 C O doub 1.21 N N
34 C13 C14 C C sing 1.51 N N
35 C14 O14 C O sing 1.43 N N
36 C14 H141 C H sing 1.09 N N
37 C14 H142 C H sing 1.09 N N
38 O14 HO14 O H sing 0.97 N N
39 C15 C16 C C sing 1.51 N N
40 C15 H151 C H sing 1.09 N N
41 C15 H152 C H sing 1.09 N N
42 C16 C17 C C sing 1.4 N Y
43 C17 O17 C O sing 1.36 N N
44 C17 C18 C C doub 1.39 N Y
45 O17 HO17 O H sing 0.97 N N
46 C18 C19 C C sing 1.47 N N
47 C19 O19 C O doub 1.22 N N
48 C19 C20 C C sing 1.48 N N
49 C21 H211 C H sing 1.09 N N
50 C21 H212 C H sing 1.09 N N
51 C21 H213 C H sing 1.09 N N
52 C1' C2' C C sing 1.53 N N
53 C1' O5' C O sing 1.43 N N
54 C1' H1' C H sing 1.09 N N
55 C2' C3' C C sing 1.53 N N
56 C2' H2'1 C H sing 1.09 N N
57 C2' H2'2 C H sing 1.09 N N
58 C3' N3' C N sing 1.47 N N
59 C3' C4' C C sing 1.53 N N
60 C3' H3' C H sing 1.09 N N
61 N3' HN'1 N H sing 1.01 N N
62 N3' HN'2 N H sing 1.01 N N
63 C4' O4' C O sing 1.43 N N
64 C4' C5' C C sing 1.53 N N
65 C4' H4' C H sing 1.09 N N
66 O4' HO4' O H sing 0.97 N N
67 C5' O5' C O sing 1.42 N N
68 C5' C6' C C sing 1.53 N N
69 C5' H5' C H sing 1.09 N N
70 C6' H6'1 C H sing 1.09 N N
71 C6' H6'2 C H sing 1.09 N N
72 C6' H6'3 C H sing 1.09 N N



DM2 : Used in PDB Entries

Total Number of PDB Entries: 12
Ligand Code PDB Entry ID Type Total Distinct
DM2 151d Open in New Window Bound ligand 1 1
DM2 1d12 Open in New Window Bound ligand 1 1
DM2 1da9 Open in New Window Bound ligand 1 1
DM2 1i1e Open in New Window Bound ligand 1 1
DM2 1p20 Open in New Window Bound ligand 1 1
DM2 2dr6 Open in New Window Bound ligand 1 1
DM2 4dx7 Open in New Window Bound ligand 3 1
DM2 4zvm Open in New Window Bound ligand 2 1
DM2 5mra Open in New Window Bound ligand 1 1
DM2 5om7 Open in New Window Bound ligand 1 1
DM2 6ftp Open in New Window Bound ligand 1 1
DM2 6kn4 Open in New Window Bound ligand 2 1