Chemical Components in the PDB

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EM9 : Summary

Code

EM9

One-letter code

X

Molecule name

N-butyl-11-[(7alpha,9beta,13alpha,14beta,16alpha,17alpha)-16-chloro-3,17-dihydroxyestra-1,3,5(10)-trien-7-yl]-N-methylundecanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 N-butyl-11-[(7alpha,9beta,13alpha,14beta,16alpha,17alpha)-16-chloro-3,17-dihydroxyestra-1,3,5(10)-trien-7-yl]-N-methylundecanamide
OpenEye OEToolkits 2.0.6 ~{N}-butyl-11-[(7~{R},8~{R},9~{S},13~{S},14~{S},16~{R},17~{R})-16-chloranyl-13-methyl-3,17-bis(oxidanyl)-6,7,8,9,11,12,14,15,16,17-decahydrocyclopenta[a]phenanthren-7-yl]-~{N}-methyl-undecanamide

Formula

C34 H54 Cl N O3

Formal charge

0

Molecular weight

560.25 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(CCCCCCCCCC(N(CCCC)C)=O)C1C3C(c2c(C1)cc(cc2)O)CCC4(C(O)C(Cl)CC34)C
SMILES CACTVS 3.385 CCCCN(C)C(=O)CCCCCCCCCC[CH]1Cc2cc(O)ccc2[CH]3CC[C]4(C)[CH](O)[CH](Cl)C[CH]4[CH]13
SMILES OpenEye OEToolkits 2.0.6 CCCCN(C)C(=O)CCCCCCCCCCC1Cc2cc(ccc2C3C1C4CC(C(C4(CC3)C)O)Cl)O
Canonical SMILES CACTVS 3.385 CCCCN(C)C(=O)CCCCCCCCCC[C@@H]1Cc2cc(O)ccc2[C@H]3CC[C@]4(C)[C@@H](O)[C@H](Cl)C[C@H]4[C@H]13
Canonical SMILES OpenEye OEToolkits 2.0.6 CCCCN(C)C(=O)CCCCCCCCCC[C@@H]1Cc2cc(ccc2[C@@H]3[C@@H]1[C@@H]4C[C@H]([C@@H]([C@]4(CC3)C)O)Cl)O

IUPAC InChI

InChI=1S/C34H54ClNO3/c1-4-5-20-36(3)31(38)15-13-11-9-7-6-8-10-12-14-24-21-25-22-26(37)16-17-27(25)28-18-19-34(2)29(32(24)28)23-30(35)33(34)39/h16-17,22,24,28-30,32-33,37,39H,4-15,18-21,23H2,1-3H3/t24-,28-,29+,30-,32-,33+,34+/m1/s1

IUPAC InChI key

FQJIZXBCOKNLMR-FTAPQOLWSA-N
EM9

wwPDB Information

Atom count

93 (39 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-06-21

Last modified at

2018-09-07

Status

Released

Obsoleted

Not Assigned



EM9 : Atoms of Molecule

Total Number of Atoms: 93
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAL C C1 N N N 0 -2.86 -0.164 0.327
2 CAK C C2 R N N 0 -4.079 -0.348 1.232
3 CAJ C C3 R N N 0 -5.352 -0.008 0.457
4 CBD C C4 N N N 0 -4.17 -1.805 1.686
5 CBE C C5 N Y N 0 -4.566 -2.708 0.548
6 CBF C C6 N Y N 0 -4.37 -4.073 0.71
7 CBG C C7 N Y N 0 -4.721 -4.96 -0.292
8 OBH O O1 N N N 0 -4.523 -6.294 -0.124
9 CBI C C8 N Y N 0 -5.277 -4.481 -1.47
10 CBJ C C9 N Y N 0 -5.467 -3.125 -1.632
11 CBK C C10 N Y N 0 -5.108 -2.235 -0.629
12 CBL C C11 S N N 0 -5.311 -0.768 -0.874
13 C49 C C12 N N N 0 -6.553 -0.498 -1.71
14 CAB C C13 N N N 0 -6.73 1.015 -1.946
15 CAC C C14 S N N 0 -6.793 1.686 -0.59
16 CAD C C15 S N N 0 -5.429 1.467 0.121
17 C9 C C16 N N N 0 -7.901 1.047 0.248
18 CAH C C17 R N N 0 -6.954 3.202 -0.58
19 OAI O O2 N N N 0 -8.337 3.553 -0.493
20 CAF C C18 R N N 0 -6.197 3.686 0.682
21 CL CL CL1 N N N 0 -4.923 4.875 0.222
22 CAE C C19 N N N 0 -5.546 2.424 1.312
23 H1 H H1 N N N 0 -2.9 -0.887 -0.488
24 H2 H H2 N N N 0 -2.86 0.846 -0.082
25 H4 H H4 N N N 0 -3.993 0.303 2.102
26 H5 H H5 N N N 0 -6.228 -0.312 1.031
27 H6 H H6 N N N 0 -3.2 -2.12 2.07
28 H7 H H7 N N N 0 -4.911 -1.886 2.481
29 H8 H H8 N N N 0 -3.938 -4.446 1.627
30 H9 H H9 N N N 0 -5.273 -6.756 0.274
31 H10 H H10 N N N 0 -5.558 -5.166 -2.256
32 H11 H H11 N N N 0 -5.9 -2.752 -2.549
33 H12 H H12 N N N 0 -4.454 -0.403 -1.441
34 H13 H H13 N N N 0 -6.457 -1.002 -2.671
35 H14 H H14 N N N 0 -7.428 -0.885 -1.188
36 H15 H H15 N N N 0 -5.882 1.402 -2.511
37 H16 H H16 N N N 0 -7.654 1.198 -2.494
38 H17 H H17 N N N 0 -4.605 1.751 -0.534
39 H18 H H18 N N N 0 -8.871 1.289 -0.186
40 H19 H H19 N N N 0 -7.769 -0.035 0.261
41 H20 H H20 N N N 0 -7.853 1.431 1.268
42 H21 H H21 N N N 0 -6.511 3.635 -1.477
43 H22 H H22 N N N 0 -8.502 4.505 -0.483
44 H23 H H23 N N N 0 -6.895 4.139 1.386
45 H24 H H24 N N N 0 -6.19 2.002 2.084
46 H25 H H25 N N N 0 -4.562 2.659 1.716
47 C1 C C20 N N N 0 -1.583 -0.385 1.141
48 C2 C C21 N N N 0 -0.363 -0.201 0.236
49 C3 C C22 N N N 0 0.914 -0.422 1.05
50 C4 C C23 N N N 0 2.134 -0.238 0.145
51 C5 C C24 N N N 0 3.41 -0.458 0.958
52 C6 C C25 N N N 0 4.63 -0.274 0.053
53 C7 C C26 N N N 0 5.907 -0.495 0.867
54 C8 C C27 N N N 0 7.127 -0.311 -0.038
55 C10 C C28 N N N 0 8.403 -0.531 0.776
56 C11 C C29 N N N 0 9.605 -0.35 -0.116
57 N1 N N1 N N N 0 10.846 -0.497 0.388
58 O1 O O3 N N N 0 9.455 -0.072 -1.287
59 C13 C C30 N N N 0 12.014 -0.321 -0.479
60 C14 C C31 N N N 0 12.453 1.144 -0.451
61 C15 C C32 N N N 0 13.673 1.328 -1.356
62 H26 H H26 N N N 0 -1.583 -1.395 1.55
63 C16 C C33 N N N 0 14.112 2.793 -1.329
64 C17 C C34 N N N 0 11.028 -0.833 1.802
65 H3 H H3 N N N 0 -1.542 0.337 1.957
66 H27 H H27 N N N 0 -0.403 -0.923 -0.579
67 H28 H H28 N N N 0 -0.363 0.809 -0.173
68 H29 H H29 N N N 0 0.954 0.301 1.865
69 H30 H H30 N N N 0 0.914 -1.432 1.459
70 H31 H H31 N N N 0 2.093 -0.96 -0.671
71 H32 H H32 N N N 0 2.133 0.773 -0.265
72 H33 H H33 N N N 0 3.451 0.264 1.774
73 H34 H H34 N N N 0 3.41 -1.469 1.367
74 H35 H H35 N N N 0 4.59 -0.997 -0.762
75 H36 H H36 N N N 0 4.63 0.736 -0.356
76 H37 H H37 N N N 0 5.947 0.228 1.682
77 H38 H H38 N N N 0 5.907 -1.505 1.276
78 H39 H H39 N N N 0 7.086 -1.033 -0.854
79 H40 H H40 N N N 0 7.126 0.699 -0.447
80 H41 H H41 N N N 0 8.444 0.191 1.591
81 H42 H H42 N N N 0 8.403 -1.542 1.185
82 H43 H H43 N N N 0 12.829 -0.951 -0.123
83 H44 H H44 N N N 0 11.755 -0.604 -1.499
84 H45 H H45 N N N 0 11.638 1.775 -0.807
85 H46 H H46 N N N 0 12.712 1.427 0.569
86 H47 H H47 N N N 0 14.488 0.698 -1.0
87 H48 H H48 N N N 0 13.414 1.045 -2.377
88 H49 H H49 N N N 0 14.981 2.924 -1.974
89 H50 H H50 N N N 0 13.297 3.424 -1.685
90 H51 H H51 N N N 0 14.371 3.076 -0.308
91 H52 H H52 N N N 0 11.049 -1.917 1.919
92 H53 H H53 N N N 0 11.967 -0.411 2.159
93 H54 H H54 N N N 0 10.201 -0.422 2.382



EM9 : Chemical Bonds

Total Number of Bonds: 96
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OBH CBG O C sing 1.36 N N
2 CBG CBF C C doub 1.38 N Y
3 CBG CBI C C sing 1.39 N Y
4 CBF CBE C C sing 1.39 N Y
5 CBI CBJ C C doub 1.38 N Y
6 CBD CBE C C sing 1.51 N N
7 CBD CAK C C sing 1.53 N N
8 CBE CBK C C doub 1.38 N Y
9 CBJ CBK C C sing 1.39 N Y
10 CBK CBL C C sing 1.5 N N
11 C9 CAC C C sing 1.53 N N
12 CAK CAJ C C sing 1.53 N N
13 CAK CAL C C sing 1.53 N N
14 CAJ CBL C C sing 1.53 N N
15 CAJ CAD C C sing 1.51 N N
16 CAE CAD C C sing 1.53 N N
17 CAE CAF C C sing 1.55 N N
18 CBL C49 C C sing 1.52 N N
19 CAD CAC C C sing 1.55 N N
20 CAF CAH C C sing 1.55 N N
21 CAF CL C CL sing 1.8 N N
22 C49 CAB C C sing 1.54 N N
23 CAC CAH C C sing 1.52 N N
24 CAC CAB C C sing 1.51 N N
25 CAH OAI C O sing 1.43 N N
26 CAL H1 C H sing 1.09 N N
27 CAL H2 C H sing 1.09 N N
28 CAK H4 C H sing 1.09 N N
29 CAJ H5 C H sing 1.09 N N
30 CBD H6 C H sing 1.09 N N
31 CBD H7 C H sing 1.09 N N
32 CBF H8 C H sing 1.08 N N
33 OBH H9 O H sing 0.97 N N
34 CBI H10 C H sing 1.08 N N
35 CBJ H11 C H sing 1.08 N N
36 CBL H12 C H sing 1.09 N N
37 C49 H13 C H sing 1.09 N N
38 C49 H14 C H sing 1.09 N N
39 CAB H15 C H sing 1.09 N N
40 CAB H16 C H sing 1.09 N N
41 CAD H17 C H sing 1.09 N N
42 C9 H18 C H sing 1.09 N N
43 C9 H19 C H sing 1.09 N N
44 C9 H20 C H sing 1.09 N N
45 CAH H21 C H sing 1.09 N N
46 OAI H22 O H sing 0.97 N N
47 CAF H23 C H sing 1.09 N N
48 CAE H24 C H sing 1.09 N N
49 CAE H25 C H sing 1.09 N N
50 CAL C1 C C sing 1.53 N N
51 C1 C2 C C sing 1.53 N N
52 C2 C3 C C sing 1.53 N N
53 C3 C4 C C sing 1.53 N N
54 C4 C5 C C sing 1.53 N N
55 C5 C6 C C sing 1.53 N N
56 C6 C7 C C sing 1.53 N N
57 C7 C8 C C sing 1.53 N N
58 C8 C10 C C sing 1.53 N N
59 C10 C11 C C sing 1.51 N N
60 C11 N1 C N sing 1.35 N N
61 C11 O1 C O doub 1.21 N N
62 N1 C13 N C sing 1.47 N N
63 C13 C14 C C sing 1.53 N N
64 C14 C15 C C sing 1.53 N N
65 C15 C16 C C sing 1.53 N N
66 N1 C17 N C sing 1.46 N N
67 C1 H3 C H sing 1.09 N N
68 C1 H26 C H sing 1.09 N N
69 C2 H27 C H sing 1.09 N N
70 C2 H28 C H sing 1.09 N N
71 C3 H29 C H sing 1.09 N N
72 C3 H30 C H sing 1.09 N N
73 C4 H31 C H sing 1.09 N N
74 C4 H32 C H sing 1.09 N N
75 C5 H33 C H sing 1.09 N N
76 C5 H34 C H sing 1.09 N N
77 C6 H35 C H sing 1.09 N N
78 C6 H36 C H sing 1.09 N N
79 C7 H37 C H sing 1.09 N N
80 C7 H38 C H sing 1.09 N N
81 C8 H39 C H sing 1.09 N N
82 C8 H40 C H sing 1.09 N N
83 C10 H41 C H sing 1.09 N N
84 C10 H42 C H sing 1.09 N N
85 C13 H43 C H sing 1.09 N N
86 C13 H44 C H sing 1.09 N N
87 C14 H45 C H sing 1.09 N N
88 C14 H46 C H sing 1.09 N N
89 C15 H47 C H sing 1.09 N N
90 C15 H48 C H sing 1.09 N N
91 C16 H49 C H sing 1.09 N N
92 C16 H50 C H sing 1.09 N N
93 C16 H51 C H sing 1.09 N N
94 C17 H52 C H sing 1.09 N N
95 C17 H53 C H sing 1.09 N N
96 C17 H54 C H sing 1.09 N N



EM9 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
EM9 6dtp Open in New Window Bound ligand 1 1