Chemical Components in the PDB

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CGM : Summary

Code

CGM

One-letter code

X

Molecule name

(4R,5S,6S,7R,9R,11E,13E,15S,16R)-16-ethyl-4-hydroxy-5,9,13,15-tetramethyl-2,10-dioxo-7-(2-oxoethyl)-1-oxacyclohexadeca-11,13-dien-6-yl 3,6-dideoxy-3-(dimethylamino)-beta-D-glucopyranoside

Systematic names

ProgramVersionName
ACDLabs 12.01 (4R,5S,6S,7R,9R,11E,13E,15S,16R)-16-ethyl-4-hydroxy-5,9,13,15-tetramethyl-2,10-dioxo-7-(2-oxoethyl)-1-oxacyclohexadeca-11,13-dien-6-yl 3,6-dideoxy-3-(dimethylamino)-beta-D-glucopyranoside
OpenEye OEToolkits 2.0.6 2-[(4~{R},5~{S},6~{S},7~{R},9~{R},11~{E},13~{E},15~{S},16~{R})-6-[(2~{R},3~{R},4~{S},5~{S},6~{R})-4-(dimethylamino)-6-methyl-3,5-bis(oxidanyl)oxan-2-yl]oxy-16-ethyl-5,9,13,15-tetramethyl-4-oxidanyl-2,10-bis(oxidanylidene)-1-oxacyclohexadeca-11,13-dien-7-yl]ethanal

Formula

C31 H51 N O9

Formal charge

0

Molecular weight

581.738 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1C(=O)OC(CC)C(C=C(C=CC(=O)C(C)CC(CC=O)C(C(C1O)C)OC2OC(C)C(C(C2O)N(C)C)O)C)C
SMILES CACTVS 3.385 CC[CH]1OC(=O)C[CH](O)[CH](C)[CH](O[CH]2O[CH](C)[CH](O)[CH]([CH]2O)N(C)C)[CH](CC=O)C[CH](C)C(=O)C=CC(=C[CH]1C)C
SMILES OpenEye OEToolkits 2.0.6 CCC1C(C=C(C=CC(=O)C(CC(C(C(C(CC(=O)O1)O)C)OC2C(C(C(C(O2)C)O)N(C)C)O)CC=O)C)C)C
Canonical SMILES CACTVS 3.385 CC[C@H]1OC(=O)C[C@@H](O)[C@H](C)[C@@H](O[C@@H]2O[C@H](C)[C@@H](O)[C@@H]([C@H]2O)N(C)C)[C@@H](CC=O)C[C@@H](C)C(=O)\C=C\C(=C\[C@@H]1C)C
Canonical SMILES OpenEye OEToolkits 2.0.6 CC[C@@H]1[C@H](/C=C(/C=C/C(=O)[C@@H](C[C@@H]([C@@H]([C@H]([C@@H](CC(=O)O1)O)C)O[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)C)O)N(C)C)O)CC=O)C)\C)C

IUPAC InChI

InChI=1S/C31H51NO9/c1-9-25-19(4)14-17(2)10-11-23(34)18(3)15-22(12-13-33)30(20(5)24(35)16-26(36)40-25)41-31-29(38)27(32(7)8)28(37)21(6)39-31/h10-11,13-14,18-22,24-25,27-31,35,37-38H,9,12,15-16H2,1-8H3/b11-10+,17-14+/t18-,19+,20+,21-,22+,24-,25-,27+,28-,29-,30-,31+/m1/s1

IUPAC InChI key

FERSDKADYZRIAA-CQGKBTLCSA-N
CGM

wwPDB Information

Atom count

92 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-09-22

Last modified at

2018-12-14

Status

Released

Obsoleted

Not Assigned



CGM : Atoms of Molecule

Total Number of Atoms: 92
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C12 S N N 0 -5.828 -0.114 -0.633
2 C1 C C13 N N N 0 -6.594 -0.487 -1.904
3 C10 C C20 S N N 0 0.912 0.804 0.454
4 C11 C C21 R N N 0 3.247 0.745 -0.084
5 C12 C C28 R N N 0 4.623 1.141 0.457
6 C13 C C25 S N N 0 5.691 0.795 -0.585
7 C14 C C27 N N N 0 8.028 1.141 -1.115
8 C15 C C26 N N N 0 7.401 0.14 0.999
9 C16 C C24 S N N 0 5.603 -0.699 -0.914
10 C17 C C22 R N N 0 4.189 -1.024 -1.401
11 C18 C C23 N N N 0 4.075 -2.525 -1.674
12 C19 C C17 R N N 0 0.456 -0.603 0.847
13 C2 C C5 R N N 0 -5.407 1.354 -0.704
14 C20 C C18 N N N 0 -0.777 -0.507 1.748
15 C21 C C19 N N N 0 -1.147 -1.882 2.242
16 C22 C C16 N N N 0 0.105 -1.396 -0.414
17 C23 C C14 R N N 0 0.18 -2.894 -0.111
18 C24 C C15 N N N 0 0.794 -3.104 1.275
19 C25 C C6 N N N 0 -1.207 -3.482 -0.14
20 C26 C C7 N N N 0 -2.328 -2.638 -0.259
21 C27 C C8 N N N 0 -3.575 -3.173 -0.288
22 C28 C C9 N N N 0 -4.748 -2.312 -0.41
23 C29 C C10 N N N 0 -6.128 -2.92 -0.426
24 C3 C C31 N N N 0 -6.582 2.242 -0.288
25 C30 C C11 N N N 0 -4.606 -0.987 -0.509
26 C4 C C4 N N N 0 -6.203 3.712 -0.479
27 C5 C C2 N N N 0 -3.454 2.588 -0.123
28 C6 C C1 N N N 0 -2.258 2.876 0.748
29 C7 C C30 R N N 0 -0.99 2.374 0.053
30 C8 C C3 S N N 0 -0.013 1.838 1.101
31 C9 C C29 N N N 0 0.824 2.993 1.656
32 H1 H H1 N N N 0 -2.18 3.951 0.914
33 H10 H H10 N N N 0 -6.147 -3.796 0.223
34 H11 H H11 N N N 0 -6.852 -2.188 -0.069
35 H12 H H12 N N N 0 -6.382 -3.217 -1.444
36 H13 H H13 N N N 0 -3.622 -0.544 -0.503
37 H14 H H14 N N N 0 -6.471 -0.266 0.235
38 H15 H H15 N N N 0 -6.992 -1.497 -1.806
39 H16 H H16 N N N 0 -7.415 0.215 -2.052
40 H17 H H17 N N N 0 -5.92 -0.443 -2.76
41 H18 H H18 N N N 0 0.799 -3.386 -0.861
42 H19 H H19 N N N 0 0.376 -4.004 1.724
43 H2 H H2 N N N 0 -2.374 2.368 1.705
44 H20 H H20 N N N 0 1.874 -3.212 1.181
45 H21 H H21 N N N 0 0.568 -2.244 1.906
46 H22 H H22 N N N 0 0.812 -1.15 -1.206
47 H23 H H23 N N N 0 -0.904 -1.14 -0.735
48 H24 H H24 N N N 0 1.259 -1.109 1.383
49 H25 H H25 N N N 0 -0.556 0.138 2.599
50 H26 H H26 N N N 0 -1.609 -0.088 1.181
51 H27 H H27 N N N 0 -1.362 -2.67 1.535
52 H28 H H28 N N N 0 0.873 0.909 -0.63
53 H29 H H29 N N N 0 3.03 1.321 -0.983
54 H3 H H3 N N N 0 -0.57 1.37 1.912
55 H30 H H30 N N N 0 3.984 -0.471 -2.318
56 H31 H H31 N N N 0 3.068 -2.756 -2.02
57 H32 H H32 N N N 0 4.797 -2.81 -2.44
58 H33 H H33 N N N 0 4.28 -3.077 -0.757
59 H34 H H34 N N N 0 5.823 -1.282 -0.019
60 H35 H H35 N N N 0 6.546 -1.951 -2.196
61 H36 H H36 N N N 0 5.52 1.378 -1.49
62 H38 H H38 N N N 0 7.522 -0.848 0.556
63 H39 H H39 N N N 0 8.342 0.451 1.454
64 H4 H H4 N N N 0 -5.334 3.947 0.136
65 H40 H H40 N N N 0 6.622 0.105 1.76
66 H41 H H41 N N N 0 7.759 1.91 -1.84
67 H42 H H42 N N N 0 9.005 1.37 -0.688
68 H43 H H43 N N N 0 8.068 0.171 -1.613
69 H44 H H44 N N N 0 4.824 0.596 1.379
70 H45 H H45 N N N 0 3.996 2.837 1.369
71 H46 H H46 N N N 0 0.162 3.773 2.032
72 H47 H H47 N N N 0 1.453 2.628 2.468
73 H48 H H48 N N N 0 1.452 3.4 0.864
74 H49 H H49 N N N 0 -1.249 1.577 -0.644
75 H5 H H5 N N N 0 -5.965 3.892 -1.528
76 H50 H H50 N N N 0 -0.944 3.841 -1.342
77 H51 H H51 N N N 0 -6.82 2.062 0.761
78 H52 H H52 N N N 0 -7.45 2.007 -0.903
79 H6 H H6 N N N 0 -7.04 4.345 -0.183
80 H7 H H7 N N N 0 -5.112 1.598 -1.724
81 H8 H H8 N N N 0 -2.195 -1.569 -0.325
82 H9 H H9 N N N 0 -3.7 -4.246 -0.219
83 N N N1 N N N 0 7.022 1.102 -0.046
84 O O O9 N N N 0 -4.287 1.584 0.191
85 O1 O O8 N N N 0 -3.663 3.261 -1.104
86 O2 O O7 N N N 0 -0.38 3.452 -0.66
87 O3 O O3 N N N 0 2.251 1.014 0.906
88 O4 O O6 N N N 0 4.648 2.546 0.717
89 O5 O O5 N N N 0 6.547 -1.019 -1.938
90 O6 O O4 N N N 0 3.243 -0.649 -0.398
91 O7 O O2 N N N 0 -1.203 -2.102 3.428
92 O8 O O1 N N N 0 -1.359 -4.684 -0.061



CGM : 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 C15 N C N sing 1.47 N N
2 C14 N C N sing 1.47 N N
3 N C13 N C sing 1.47 N N
4 O5 C16 O C sing 1.43 N N
5 C16 C13 C C sing 1.53 N N
6 C16 C17 C C sing 1.53 N N
7 C13 C12 C C sing 1.53 N N
8 C12 O4 C O sing 1.43 N N
9 C12 C11 C C sing 1.53 N N
10 C18 C17 C C sing 1.53 N N
11 C17 O6 C O sing 1.43 N N
12 O6 C11 O C sing 1.43 N N
13 C11 O3 C O sing 1.43 N N
14 O3 C10 O C sing 1.43 N N
15 C24 C23 C C sing 1.53 N N
16 C22 C23 C C sing 1.53 N N
17 C22 C19 C C sing 1.53 N N
18 C20 C19 C C sing 1.53 N N
19 C20 C21 C C sing 1.51 N N
20 C23 C25 C C sing 1.51 N N
21 C10 C19 C C sing 1.53 N N
22 C10 C8 C C sing 1.53 N N
23 C9 C8 C C sing 1.53 N N
24 C21 O7 C O doub 1.21 N N
25 C8 C7 C C sing 1.53 N N
26 C25 O8 C O doub 1.21 N N
27 C25 C26 C C sing 1.41 N N
28 C26 C27 C C doub 1.36 E N
29 C7 O2 C O sing 1.43 N N
30 C7 C6 C C sing 1.53 N N
31 C6 C5 C C sing 1.51 N N
32 C27 C28 C C sing 1.46 N N
33 C29 C28 C C sing 1.51 N N
34 C28 C30 C C doub 1.34 E N
35 C5 O1 C O doub 1.21 N N
36 C5 O C O sing 1.34 N N
37 O C2 O C sing 1.45 N N
38 C30 C C C sing 1.51 N N
39 C C2 C C sing 1.53 N N
40 C C1 C C sing 1.53 N N
41 C2 C3 C C sing 1.53 N N
42 C3 C4 C C sing 1.53 N N
43 C6 H1 C H sing 1.09 N N
44 C6 H2 C H sing 1.09 N N
45 C8 H3 C H sing 1.09 N N
46 C4 H4 C H sing 1.09 N N
47 C4 H5 C H sing 1.09 N N
48 C4 H6 C H sing 1.09 N N
49 C2 H7 C H sing 1.09 N N
50 C26 H8 C H sing 1.08 N N
51 C27 H9 C H sing 1.08 N N
52 C29 H10 C H sing 1.09 N N
53 C29 H11 C H sing 1.09 N N
54 C29 H12 C H sing 1.09 N N
55 C30 H13 C H sing 1.08 N N
56 C H14 C H sing 1.09 N N
57 C1 H15 C H sing 1.09 N N
58 C1 H16 C H sing 1.09 N N
59 C1 H17 C H sing 1.09 N N
60 C23 H18 C H sing 1.09 N N
61 C24 H19 C H sing 1.09 N N
62 C24 H20 C H sing 1.09 N N
63 C24 H21 C H sing 1.09 N N
64 C22 H22 C H sing 1.09 N N
65 C22 H23 C H sing 1.09 N N
66 C19 H24 C H sing 1.09 N N
67 C20 H25 C H sing 1.09 N N
68 C20 H26 C H sing 1.09 N N
69 C21 H27 C H sing 1.08 N N
70 C10 H28 C H sing 1.09 N N
71 C11 H29 C H sing 1.09 N N
72 C17 H30 C H sing 1.09 N N
73 C18 H31 C H sing 1.09 N N
74 C18 H32 C H sing 1.09 N N
75 C18 H33 C H sing 1.09 N N
76 C16 H34 C H sing 1.09 N N
77 O5 H35 O H sing 0.97 N N
78 C13 H36 C H sing 1.09 N N
79 C15 H38 C H sing 1.09 N N
80 C15 H39 C H sing 1.09 N N
81 C15 H40 C H sing 1.09 N N
82 C14 H41 C H sing 1.09 N N
83 C14 H42 C H sing 1.09 N N
84 C14 H43 C H sing 1.09 N N
85 C12 H44 C H sing 1.09 N N
86 O4 H45 O H sing 0.97 N N
87 C9 H46 C H sing 1.09 N N
88 C9 H47 C H sing 1.09 N N
89 C9 H48 C H sing 1.09 N N
90 C7 H49 C H sing 1.09 N N
91 O2 H50 O H sing 0.97 N N
92 C3 H51 C H sing 1.09 N N
93 C3 H52 C H sing 1.09 N N



CGM : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
CGM 6b11 Open in New Window Bound ligand 2 1