Chemical Components in the PDB

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MT9 : Summary

Code

MT9

One-letter code

X

Molecule name

(3R,4S,5S,7R,9E,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside

Synonyms

methymycin

Systematic names

ProgramVersionName
ACDLabs 10.04 (3R,4S,5S,7R,9E,11S,12R)-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-2,8-dioxooxacyclododec-9-en-4-yl 3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranoside
OpenEye OEToolkits 1.5.0 (3R,4S,5S,7R,9E,11S,12R)-4-[(2S,3R,4S,6R)-4-dimethylamino-3-hydroxy-6-methyl-oxan-2-yl]oxy-12-ethyl-11-hydroxy-3,5,7,11-tetramethyl-1-oxacyclododec-9-ene-2,8-dione

Formula

C25 H43 N O7

Formal charge

0

Molecular weight

469.611 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C2OC(CC)C(O)(C=CC(=O)C(C)CC(C(OC1OC(CC(N(C)C)C1O)C)C2C)C)C
SMILES CACTVS 3.341 CC[CH]1OC(=O)[CH](C)[CH](O[CH]2O[CH](C)C[CH]([CH]2O)N(C)C)[CH](C)C[CH](C)C(=O)C=C[C]1(C)O
SMILES OpenEye OEToolkits 1.5.0 CCC1C(C=CC(=O)C(CC(C(C(C(=O)O1)C)OC2C(C(CC(O2)C)N(C)C)O)C)C)(C)O
Canonical SMILES CACTVS 3.341 CC[C@H]1OC(=O)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)C[C@@H]([C@H]2O)N(C)C)[C@@H](C)C[C@@H](C)C(=O)/C=C/[C@]1(C)O
Canonical SMILES OpenEye OEToolkits 1.5.0 CC[C@@H]1[C@@](\C=C\C(=O)[C@@H](C[C@@H]([C@@H]([C@H](C(=O)O1)C)O[C@H]2[C@@H]([C@H](C[C@H](O2)C)N(C)C)O)C)C)(C)O

IUPAC InChI

InChI=1S/C25H43NO7/c1-9-20-25(6,30)11-10-19(27)14(2)12-15(3)22(17(5)23(29)32-20)33-24-21(28)18(26(7)8)13-16(4)31-24/h10-11,14-18,20-22,24,28,30H,9,12-13H2,1-8H3/b11-10+/t14-,15+,16-,17-,18+,20-,21-,22+,24+,25+/m1/s1

IUPAC InChI key

HUKYPYXOBINMND-HYUJHOPRSA-N
MT9

wwPDB Information

Atom count

76 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2009-04-22

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



MT9 : Atoms of Molecule

Total Number of Atoms: 76
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C4 S N N 0 4.149 -1.021 0.892
2 C3 C C3 R N N 0 3.087 -1.753 0.064
3 O3 O O3 N N N 0 2.28 -0.786 -0.657
4 C13 C C13 N N N 0 1.699 -1.179 -1.796
5 O2 O O2 N N N 0 1.798 -2.337 -2.147
6 C5 C C5 N N N 0 3.476 0.074 1.685
7 C12 C C12 R N N 0 0.941 -0.217 -2.67
8 C11 C C11 S N N 0 -0.001 0.663 -1.863
9 C10 C C10 S N N 0 0.677 1.881 -1.25
10 C9 C C9 N N N 0 0.222 2.077 0.2
11 C8 C C8 R N N 0 1.204 2.996 0.935
12 C7 C C7 N N N 0 2.158 2.13 1.726
13 C6 C C6 N N N 0 2.868 1.061 1.031
14 O1 O O1 N N N 0 2.322 2.326 2.908
15 O7 O O7 N N N 0 5.129 -0.453 0.024
16 C25 C C25 N N N 0 4.816 -2.011 1.847
17 C2 C C2 N N N 0 2.192 -2.569 0.999
18 C24 C C24 N N N 0 0.431 3.902 1.894
19 C23 C C23 N N N 0 0.274 3.13 -2.05
20 O4 O O4 N N N 0 -0.624 -0.124 -0.843
21 C14 C C14 N N N 0 1.907 0.595 -3.527
22 C16 C C16 R N N 0 -2.606 -1.084 0.157
23 C15 C C15 S N N 0 -2.052 -0.126 -0.902
24 O5 O O5 N N N 0 -2.542 1.193 -0.652
25 C19 C C19 R N N 0 -3.965 1.309 -0.713
26 C18 C C18 N N N 0 -4.595 0.409 0.353
27 C17 C C17 S N N 0 -4.136 -1.035 0.128
28 O6 O O6 N N N 0 -2.165 -2.413 -0.124
29 C20 C C20 N N N 0 -4.37 2.762 -0.459
30 N1 N N1 N N N 0 -4.676 -1.893 1.191
31 C21 C C21 N N N 0 -4.433 -1.306 2.516
32 C22 C C22 N N N 0 -6.107 -2.151 0.984
33 C1 C C1 N N N 0 1.222 -3.413 0.169
34 H3 H H3 N N N 0 3.576 -2.42 -0.645
35 H5 H H5 N N N 0 3.496 0.049 2.763
36 H12 H H12 N N N 0 0.324 -0.824 -3.362
37 H11 H H11 N N N 0 -0.8 1.016 -2.537
38 H10 H H10 N N N 0 1.757 1.78 -1.265
39 H9 H H9 N N N 0 -0.772 2.519 0.216
40 H9A H H9A N N N 0 0.202 1.116 0.714
41 H8 H H8 N N N 0 1.764 3.598 0.228
42 H6 H H6 N N N 0 2.925 1.087 -0.053
43 HO7 H HO7 N N N 0 5.832 0.025 0.484
44 H25 H H25 N N N 0 5.288 -2.808 1.273
45 H25A H H25A N N N 0 5.572 -1.492 2.438
46 H25B H H25B N N N 0 4.065 -2.437 2.513
47 H2 H H2 N N N 0 2.809 -3.225 1.613
48 H2A H H2A N N N 0 1.627 -1.894 1.643
49 H24 H H24 N N N 0 -0.106 3.29 2.619
50 H24A H H24A N N N 0 1.129 4.557 2.417
51 H24B H H24B N N N 0 -0.28 4.506 1.33
52 H23 H H23 N N N 0 -0.808 3.252 -2.013
53 H23A H H23A N N N 0 0.754 4.008 -1.619
54 H23B H H23B N N N 0 0.591 3.015 -3.087
55 H14 H H14 N N N 0 2.487 -0.078 -4.158
56 H14A H H14A N N N 0 1.344 1.286 -4.153
57 H14B H H14B N N N 0 2.581 1.157 -2.88
58 H19 H H19 N N N 0 -4.312 1.001 -1.699
59 H16 H H16 N N N 0 -2.25 -0.782 1.142
60 H15 H H15 N N N 0 -2.375 -0.453 -1.891
61 H18 H H18 N N N 0 -4.28 0.741 1.343
62 H18A H H18A N N N 0 -5.681 0.462 0.279
63 H17 H H17 N N N 0 -4.494 -1.384 -0.841
64 HO6 H HO6 N N N 0 -1.223 -2.558 0.039
65 H20 H H20 N N N 0 -3.92 3.402 -1.218
66 H20A H H20A N N N 0 -5.455 2.85 -0.506
67 H20B H H20B N N N 0 -4.022 3.069 0.527
68 H21 H H21 N N N 0 -4.916 -0.331 2.575
69 H21A H H21A N N N 0 -4.842 -1.962 3.284
70 H21B H H21B N N N 0 -3.36 -1.19 2.671
71 H22 H H22 N N N 0 -6.249 -2.668 0.035
72 H22A H H22A N N N 0 -6.485 -2.772 1.796
73 H22B H H22B N N N 0 -6.648 -1.205 0.968
74 H1 H H1 N N N 0 0.65 -2.763 -0.493
75 H1B H H1B N N N 0 0.541 -3.944 0.835
76 H1A H H1A N N N 0 1.784 -4.133 -0.426



MT9 : Chemical Bonds

Total Number of Bonds: 77
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C4 C3 C C sing 1.53 N N
2 C4 C5 C C sing 1.51 N N
3 C4 O7 C O sing 1.43 N N
4 C4 C25 C C sing 1.53 N N
5 C3 O3 C O sing 1.45 N N
6 C3 C2 C C sing 1.53 N N
7 O3 C13 O C sing 1.34 N N
8 C13 O2 C O doub 1.21 N N
9 C13 C12 C C sing 1.5 N N
10 C5 C6 C C doub 1.33 N N
11 C12 C11 C C sing 1.52 E N
12 C12 C14 C C sing 1.53 N N
13 C11 C10 C C sing 1.52 N N
14 C11 O4 C O sing 1.43 N N
15 C10 C9 C C sing 1.53 N N
16 C10 C23 C C sing 1.54 N N
17 C9 C8 C C sing 1.53 N N
18 C8 C7 C C sing 1.51 N N
19 C8 C24 C C sing 1.53 N N
20 C7 C6 C C sing 1.46 N N
21 C7 O1 C O doub 1.21 N N
22 C2 C1 C C sing 1.53 N N
23 O4 C15 O C sing 1.43 N N
24 C16 C15 C C sing 1.53 N N
25 C16 C17 C C sing 1.53 N N
26 C16 O6 C O sing 1.43 N N
27 C15 O5 C O sing 1.43 N N
28 O5 C19 O C sing 1.43 N N
29 C19 C18 C C sing 1.53 N N
30 C19 C20 C C sing 1.53 N N
31 C18 C17 C C sing 1.53 N N
32 C17 N1 C N sing 1.47 N N
33 N1 C21 N C sing 1.47 N N
34 N1 C22 N C sing 1.47 N N
35 C3 H3 C H sing 1.09 N N
36 C5 H5 C H sing 1.08 N N
37 C12 H12 C H sing 1.11 N N
38 C11 H11 C H sing 1.1 N N
39 C10 H10 C H sing 1.08 N N
40 C9 H9 C H sing 1.09 N N
41 C9 H9A C H sing 1.09 N N
42 C8 H8 C H sing 1.08 N N
43 C6 H6 C H sing 1.09 N N
44 O7 HO7 O H sing 0.97 N N
45 C25 H25 C H sing 1.09 N N
46 C25 H25A C H sing 1.09 N N
47 C25 H25B C H sing 1.09 N N
48 C2 H2 C H sing 1.09 N N
49 C2 H2A C H sing 1.09 N N
50 C24 H24 C H sing 1.09 N N
51 C24 H24A C H sing 1.09 N N
52 C24 H24B C H sing 1.09 N N
53 C23 H23 C H sing 1.09 N N
54 C23 H23A C H sing 1.09 N N
55 C23 H23B C H sing 1.09 N N
56 C14 H14 C H sing 1.09 N N
57 C14 H14A C H sing 1.09 N N
58 C14 H14B C H sing 1.09 N N
59 C16 H16 C H sing 1.09 N N
60 C15 H15 C H sing 1.09 N N
61 C19 H19 C H sing 1.09 N N
62 C18 H18 C H sing 1.09 N N
63 C18 H18A C H sing 1.09 N N
64 C17 H17 C H sing 1.09 N N
65 O6 HO6 O H sing 0.97 N N
66 C20 H20 C H sing 1.09 N N
67 C20 H20A C H sing 1.09 N N
68 C20 H20B C H sing 1.09 N N
69 C21 H21 C H sing 1.09 N N
70 C21 H21A C H sing 1.09 N N
71 C21 H21B C H sing 1.09 N N
72 C22 H22 C H sing 1.09 N N
73 C22 H22A C H sing 1.09 N N
74 C22 H22B C H sing 1.09 N N
75 C1 H1 C H sing 1.09 N N
76 C1 H1A C H sing 1.09 N N
77 C1 H1B C H sing 1.09 N N



MT9 : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
MT9 3fwo Open in New Window Bound ligand 1 1
MT9 5wis Open in New Window Bound ligand 2 1