Chemical Components in the PDB

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MYM : Summary

Code

MYM

One-letter code

X

Molecule name

S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (5beta,7alpha,8alpha,10alpha,12alpha)-7-hydroxyatis-16-ene-18-thioate

Systematic names

ProgramVersionName
ACDLabs 12.01 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] (5beta,7alpha,8alpha,10alpha,12alpha)-7-hydroxyatis-16-ene-18-thioate

Formula

C31 H51 N2 O9 P S

Formal charge

0

Molecular weight

658.783 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(CNC(CCNC(C(C(COP(O)(O)=O)(C)C)O)=O)=O)SC(=O)C1(C)CCCC4(C)C1CC(O)C32C4CC(/C(C2)=C)CC3
SMILES CACTVS 3.385 CC(C)(CO[P](O)(O)=O)[CH](O)C(=O)NCCC(=O)NCCSC(=O)[C]1(C)CCC[C]2(C)[CH]1C[CH](O)[C]34CC[CH](C[CH]23)C(=C)C4
SMILES OpenEye OEToolkits 2.0.7 CC12CCCC(C1CC(C34C2CC(CC3)C(=C)C4)O)(C)C(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)O)O
Canonical SMILES CACTVS 3.385 CC(C)(CO[P](O)(O)=O)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)[C@]1(C)CCC[C@]2(C)[C@@H]1C[C@@H](O)[C@@]34CC[C@@H](C[C@@H]23)C(=C)C4
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@@]12CCC[C@@]([C@H]1C[C@H]([C@]34[C@H]2C[C@H](CC3)C(=C)C4)O)(C)C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)O)O

IUPAC InChI

InChI=1S/C31H51N2O9PS/c1-19-17-31-11-7-20(19)15-22(31)29(4)9-6-10-30(5,21(29)16-23(31)34)27(38)44-14-13-32-24(35)8-12-33-26(37)25(36)28(2,3)18-42-43(39,40)41/h20-23,25,34,36H,1,6-18H2,2-5H3,(H,32,35)(H,33,37)(H2,39,40,41)/t20-,21-,22-,23+,25-,29+,30+,31+/m0/s1

IUPAC InChI key

PHQDCKXVLPNCFQ-HHFPKWFXSA-N
MYM

wwPDB Information

Atom count

95 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-04-24

Last modified at

2019-07-19

Status

Released

Obsoleted

Not Assigned



MYM : Atoms of Molecule

Total Number of Atoms: 95
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N N N 0 1.229 -1.315 -0.475
2 C13 C C2 N N N 0 -3.489 -1.114 0.859
3 C15 C C3 N N N 0 -7.147 -1.57 1.346
4 C17 C C4 N N N 0 -8.528 0.435 1.822
5 C20 C C5 N N N 0 -8.942 0.42 0.349
6 C21 C C6 N N N 0 5.06 -1.407 -3.148
7 C22 C C7 N N N 0 5.62 -2.934 -1.301
8 C24 C C8 N N N 0 7.349 -2.151 0.326
9 C26 C C9 N N N 0 5.847 -0.427 1.299
10 C28 C C10 N N N 0 8.747 0.071 1.711
11 O04 O O1 N N N 0 -11.159 1.409 -1.857
12 P01 P P1 N N N 0 -9.737 2.106 -1.566
13 O05 O O2 N N N 0 -8.736 1.608 -2.535
14 O06 O O3 N N N 0 -9.882 3.703 -1.715
15 O03 O O4 N N N 0 -9.261 1.748 -0.07
16 C18 C C11 N N N 0 -7.302 1.333 1.998
17 C19 C C12 N N N 0 -9.682 0.974 2.67
18 C16 C C13 R N N 0 -8.187 -0.988 2.27
19 O02 O O5 N N N 0 -9.365 -1.796 2.23
20 O07 O O6 N N N 0 -7.46 -2.421 0.541
21 N02 N N1 N N N 0 -5.871 -1.143 1.415
22 C14 C C14 N N N 0 -4.84 -1.781 0.592
23 C12 C C15 N N N 0 -2.429 -1.77 0.012
24 O08 O O7 N N N 0 -2.725 -2.682 -0.73
25 N01 N N2 N N N 0 -1.152 -1.344 0.081
26 C11 C C16 N N N 0 -0.122 -1.982 -0.742
27 S01 S S1 N N N 0 2.502 -2.103 -1.492
28 C09 C C17 N N N 0 3.871 -1.193 -1.013
29 O09 O O8 N N N 0 3.753 -0.307 -0.192
30 C08 C C18 R N N 0 5.221 -1.492 -1.61
31 C07 C C19 S N N 0 6.282 -0.498 -1.195
32 C06 C C20 N N N 0 5.837 0.954 -1.363
33 C05 C C21 R N N 0 7.087 1.84 -1.315
34 O01 O O9 N N N 0 6.702 3.203 -1.5
35 C23 C C22 N N N 0 6.172 -3.097 0.108
36 C25 C C23 S N N 0 6.867 -0.696 0.198
37 C27 C C24 S N N 0 8.08 0.223 0.348
38 C29 C C25 S N N 0 9.021 1.462 2.302
39 C30 C C26 N N N 0 7.675 2.173 2.487
40 C31 C C27 N N N 0 7.028 2.401 1.122
41 C04 C C28 R N N 0 7.804 1.682 0.024
42 C03 C C29 N N N 0 9.18 2.388 -0.091
43 C02 C C30 N N N 0 9.823 2.252 1.279
44 C01 C C31 N N N 0 10.99 2.782 1.56
45 H1 H H1 N N N 0 1.167 -0.256 -0.727
46 H2 H H2 N N N 0 1.486 -1.423 0.578
47 H3 H H3 N N N 0 -3.551 -0.055 0.607
48 H4 H H4 N N N 0 -3.232 -1.222 1.912
49 H5 H H5 N N N 0 -8.12 0.036 -0.256
50 H6 H H6 N N N 0 -9.815 -0.22 0.223
51 H7 H H7 N N N 0 4.287 -2.104 -3.471
52 H8 H H8 N N N 0 4.774 -0.393 -3.427
53 H9 H H9 N N N 0 6.004 -1.663 -3.628
54 H10 H H10 N N N 0 4.74 -3.577 -1.419
55 H11 H H11 N N N 0 6.374 -3.259 -2.025
56 H12 H H12 N N N 0 7.767 -2.304 1.32
57 H13 H H13 N N N 0 8.115 -2.338 -0.426
58 H14 H H14 N N N 0 6.35 -0.417 2.266
59 H15 H H15 N N N 0 5.372 0.539 1.127
60 H16 H H16 N N N 0 5.089 -1.211 1.292
61 H17 H H17 N N N 0 8.144 -0.507 2.399
62 H18 H H18 N N N 0 9.708 -0.441 1.577
63 H19 H H19 N N N 0 -11.865 1.689 -1.258
64 H20 H H20 N N N 0 -10.167 3.991 -2.593
65 H21 H H21 N N N 0 -6.53 1.037 1.288
66 H22 H H22 N N N 0 -7.583 2.371 1.817
67 H23 H H23 N N N 0 -6.92 1.231 3.014
68 H24 H H24 N N N 0 -9.367 1.039 3.711
69 H25 H H25 N N N 0 -9.964 1.964 2.313
70 H26 H H26 N N N 0 -10.536 0.301 2.591
71 H27 H H27 N N N 0 -7.797 -0.965 3.287
72 H28 H H28 N N N 0 -9.767 -1.862 1.353
73 H29 H H29 N N N 0 -5.634 -0.414 2.009
74 H30 H H30 N N N 0 -5.097 -1.673 -0.461
75 H31 H H31 N N N 0 -4.778 -2.84 0.844
76 H32 H H32 N N N 0 -0.916 -0.615 0.675
77 H33 H H33 N N N 0 -0.379 -1.874 -1.795
78 H34 H H34 N N N 0 -0.06 -3.041 -0.49
79 H35 H H35 N N N 0 7.138 -0.635 -1.905
80 H36 H H36 N N N 0 5.354 1.093 -2.332
81 H37 H H37 N N N 0 5.149 1.253 -0.58
82 H38 H H38 N N N 0 7.76 1.544 -2.123
83 H39 H H39 N N N 0 6.258 3.376 -2.341
84 H40 H H40 N N N 0 5.394 -2.938 0.848
85 H41 H H41 N N N 0 6.533 -4.13 0.226
86 H42 H H42 N N N 0 8.825 -0.13 -0.403
87 H43 H H43 N N N 0 9.557 1.384 3.245
88 H44 H H44 N N N 0 7.022 1.562 3.108
89 H45 H H45 N N N 0 7.84 3.135 2.975
90 H46 H H46 N N N 0 5.988 2.108 1.134
91 H47 H H47 N N N 0 7.063 3.483 0.913
92 H48 H H48 N N N 0 9.782 1.889 -0.846
93 H49 H H49 N N N 0 9.032 3.436 -0.342
94 H51 H H51 N N N 0 11.413 2.665 2.546
95 H52 H H52 N N N 0 11.527 3.336 0.804



MYM : Chemical Bonds

Total Number of Bonds: 98
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O05 P01 O P doub 1.48 N N
2 O04 P01 O P sing 1.61 N N
3 P01 O06 P O sing 1.61 N N
4 P01 O03 P O sing 1.61 N N
5 C18 C17 C C sing 1.53 N N
6 C19 C17 C C sing 1.53 N N
7 C20 O03 C O sing 1.43 N N
8 C20 C17 C C sing 1.53 N N
9 C17 C16 C C sing 1.53 N N
10 C16 C15 C C sing 1.51 N N
11 C16 O02 C O sing 1.43 N N
12 O07 C15 O C doub 1.21 N N
13 C15 N02 C N sing 1.35 N N
14 N02 C14 N C sing 1.47 N N
15 C14 C13 C C sing 1.53 N N
16 C13 C12 C C sing 1.51 N N
17 C12 N01 C N sing 1.35 N N
18 C12 O08 C O doub 1.21 N N
19 N01 C11 N C sing 1.46 N N
20 C10 C11 C C sing 1.53 N N
21 C10 S01 C S sing 1.81 N N
22 S01 C09 S C sing 1.71 N N
23 C23 C22 C C sing 1.52 N N
24 C23 C24 C C sing 1.53 N N
25 C09 O09 C O doub 1.21 N N
26 C09 C08 C C sing 1.51 N N
27 C22 C08 C C sing 1.53 N N
28 C08 C21 C C sing 1.55 N N
29 C08 C07 C C sing 1.51 N N
30 C26 C25 C C sing 1.52 N N
31 C24 C25 C C sing 1.54 N N
32 C25 C07 C C sing 1.52 N N
33 C25 C27 C C sing 1.53 N N
34 C07 C06 C C sing 1.53 N N
35 C06 C05 C C sing 1.53 N N
36 C28 C27 C C sing 1.53 N N
37 C28 C29 C C sing 1.54 N N
38 C27 C04 C C sing 1.52 N N
39 C31 C30 C C sing 1.53 N N
40 C31 C04 C C sing 1.52 N N
41 C30 C29 C C sing 1.53 N N
42 C04 C05 C C sing 1.53 N N
43 C04 C03 C C sing 1.55 N N
44 C29 C02 C C sing 1.52 N N
45 C05 O01 C O sing 1.43 N N
46 C02 C03 C C sing 1.52 N N
47 C02 C01 C C doub 1.31 N N
48 C10 H1 C H sing 1.09 N N
49 C10 H2 C H sing 1.09 N N
50 C13 H3 C H sing 1.09 N N
51 C13 H4 C H sing 1.09 N N
52 C20 H5 C H sing 1.09 N N
53 C20 H6 C H sing 1.09 N N
54 C21 H7 C H sing 1.09 N N
55 C21 H8 C H sing 1.09 N N
56 C21 H9 C H sing 1.09 N N
57 C22 H10 C H sing 1.1 N N
58 C22 H11 C H sing 1.09 N N
59 C24 H12 C H sing 1.09 N N
60 C24 H13 C H sing 1.09 N N
61 C26 H14 C H sing 1.09 N N
62 C26 H15 C H sing 1.09 N N
63 C26 H16 C H sing 1.09 N N
64 C28 H17 C H sing 1.08 N N
65 C28 H18 C H sing 1.1 N N
66 O04 H19 O H sing 0.97 N N
67 O06 H20 O H sing 0.97 N N
68 C18 H21 C H sing 1.09 N N
69 C18 H22 C H sing 1.09 N N
70 C18 H23 C H sing 1.09 N N
71 C19 H24 C H sing 1.09 N N
72 C19 H25 C H sing 1.09 N N
73 C19 H26 C H sing 1.09 N N
74 C16 H27 C H sing 1.09 N N
75 O02 H28 O H sing 0.97 N N
76 N02 H29 N H sing 0.97 N N
77 C14 H30 C H sing 1.09 N N
78 C14 H31 C H sing 1.09 N N
79 N01 H32 N H sing 0.97 N N
80 C11 H33 C H sing 1.09 N N
81 C11 H34 C H sing 1.09 N N
82 C07 H35 C H sing 1.12 N N
83 C06 H36 C H sing 1.09 N N
84 C06 H37 C H sing 1.08 N N
85 C05 H38 C H sing 1.09 N N
86 O01 H39 O H sing 0.97 N N
87 C23 H40 C H sing 1.09 N N
88 C23 H41 C H sing 1.1 N N
89 C27 H42 C H sing 1.12 N N
90 C29 H43 C H sing 1.09 N N
91 C30 H44 C H sing 1.09 N N
92 C30 H45 C H sing 1.09 N N
93 C31 H46 C H sing 1.08 N N
94 C31 H47 C H sing 1.1 N N
95 C03 H48 C H sing 1.09 N N
96 C03 H49 C H sing 1.09 N N
97 C01 H51 C H sing 1.08 N N
98 C01 H52 C H sing 1.08 N N



MYM : Used in PDB Entries

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