Chemical Components in the PDB

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H8Q : Summary

Code

H8Q

One-letter code

X

Molecule name

~{N}-[(3~{S},6~{R},12~{R},15~{S},16~{S},19~{S},22~{S},25~{S})-25-[[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]sulfanylmethyl]-3-[[4-(dimethylamino)phenyl]methyl]-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptakis(oxidanylidene)-19-phenyl-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-pyridine-2-carboxamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 ~{N}-[(3~{S},6~{R},12~{R},15~{S},16~{S},19~{S},22~{S},25~{S})-25-[[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]sulfanylmethyl]-3-[[4-(dimethylamino)phenyl]methyl]-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptakis(oxidanylidene)-19-phenyl-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-pyridine-2-carboxamide

Formula

C53 H67 N9 O10 S

Formal charge

0

Molecular weight

1022.218 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC[CH]1NC(=O)[CH](NC(=O)c2ncccc2O)[CH](C)OC(=O)[CH](NC(=O)[CH]3CC(=O)[CH](CS[CH]4CN5CCC4CC5)CN3C(=O)[CH](Cc6ccc(cc6)N(C)C)N(C)C(=O)[CH]7CCCN7C1=O)c8ccccc8
SMILES OpenEye OEToolkits 2.0.6 CCC1C(=O)N2CCCC2C(=O)N(C(C(=O)N3CC(C(=O)CC3C(=O)NC(C(=O)OC(C(C(=O)N1)NC(=O)c4c(cccn4)O)C)c5ccccc5)CSC6CN7CCC6CC7)Cc8ccc(cc8)N(C)C)C
Canonical SMILES CACTVS 3.385 CC[C@H]1NC(=O)[C@@H](NC(=O)c2ncccc2O)[C@H](C)OC(=O)[C@@H](NC(=O)[C@@H]3CC(=O)[C@@H](CS[C@@H]4CN5CCC4CC5)CN3C(=O)[C@H](Cc6ccc(cc6)N(C)C)N(C)C(=O)[C@H]7CCCN7C1=O)c8ccccc8
Canonical SMILES OpenEye OEToolkits 2.0.6 CC[C@@H]1C(=O)N2CCC[C@@H]2C(=O)N([C@H](C(=O)N3C[C@@H](C(=O)C[C@H]3C(=O)N[C@H](C(=O)O[C@H]([C@@H](C(=O)N1)NC(=O)c4c(cccn4)O)C)c5ccccc5)CS[C@@H]6CN7CCC6CC7)Cc8ccc(cc8)N(C)C)C

IUPAC InChI

InChI=1S/C53H67N9O10S/c1-6-37-50(68)61-23-11-14-38(61)51(69)59(5)40(26-32-16-18-36(19-17-32)58(3)4)52(70)62-28-35(30-73-43-29-60-24-20-33(43)21-25-60)42(64)27-39(62)47(65)57-45(34-12-8-7-9-13-34)53(71)72-31(2)44(48(66)55-37)56-49(67)46-41(63)15-10-22-54-46/h7-10,12-13,15-19,22,31,33,35,37-40,43-45,63H,6,11,14,20-21,23-30H2,1-5H3,(H,55,66)(H,56,67)(H,57,65)/t31-,35+,37+,38+,39-,40-,43+,44-,45-/m0/s1

IUPAC InChI key

WTHRRGMBUAHGNI-QGNGWGIWSA-N
H8Q

wwPDB Information

Atom count

140 (73 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-11-26

Last modified at

2020-09-16

Status

Released

Obsoleted

Not Assigned



H8Q : Atoms of Molecule

Total Number of Atoms: 140
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 S N N 0 1.572 0.893 0.079
2 C3 C C2 N N N 0 3.03 1.331 0.045
3 C5 C C3 N Y N 0 3.118 3.656 0.966
4 C6 C C4 N Y N 0 3.19 5.025 0.8
5 C7 C C5 N Y N 0 3.246 5.567 -0.477
6 C8 C C6 N Y N 0 3.23 4.729 -1.585
7 C9 C C7 N Y N 0 3.158 3.361 -1.413
8 O1 O O1 N N N 0 0.721 -1.052 -0.821
9 C1 C C8 N N N 0 1.402 -0.582 0.106
10 C11 C C9 N N N 0 3.335 7.834 0.521
11 C12 C C10 N N N 0 3.378 7.521 -1.996
12 C14 C C11 N N N 0 3.001 -1.273 1.889
13 C15 C C12 S N N 0 4.17 -2.167 1.466
14 C16 C C13 N N N 0 3.668 -3.2 0.489
15 C17 C C14 N N N 0 2.348 -3.879 0.759
16 C18 C C15 S N N 0 1.26 -2.827 0.973
17 C20 C C16 N N N 0 5.263 -1.326 0.807
18 C22 C C17 S N N 0 7.867 -1.218 -0.319
19 C23 C C18 N N N 0 9.198 -1.932 -0.589
20 C24 C C19 N N N 0 8.941 -3.096 -1.554
21 C25 C C20 N N N 0 10.156 -0.941 -1.262
22 C26 C C21 N N N 0 7.296 -0.717 -1.648
23 C27 C C22 N N N 0 8.341 -2.542 -2.849
24 C28 C C23 N N N 0 9.522 -0.447 -2.566
25 C30 C C24 N N N 0 0.601 -3.05 2.305
26 C33 C C25 S N N 0 -1.576 -2.754 1.25
27 C34 C C26 N N N 0 -2.85 -2.065 1.698
28 C35 C C27 N Y N 0 -1.949 -4.058 0.587
29 C36 C C28 N Y N 0 -2.296 -5.151 1.359
30 C37 C C29 N Y N 0 -2.639 -6.345 0.752
31 C38 C C30 N Y N 0 -2.634 -6.446 -0.627
32 C39 C C31 N Y N 0 -2.288 -5.352 -1.399
33 C4 C C32 N Y N 0 3.102 2.824 -0.139
34 C40 C C33 N Y N 0 -1.95 -4.157 -0.792
35 C43 C C34 S N N 0 -5.295 -2.15 1.815
36 C44 C C35 N N N 0 -5.375 -1.98 3.326
37 C45 C C36 S N N 0 -5.774 -0.919 1.064
38 C46 C C37 N N N 0 -5.03 0.338 1.404
39 C50 C C38 N N N 0 -6.464 -0.51 -1.243
40 C51 C C39 N Y N 0 -6.364 -0.773 -2.694
41 C53 C C40 N Y N 0 -5.373 -1.933 -4.425
42 C54 C C41 N Y N 0 -6.155 -1.28 -5.367
43 C55 C C42 N Y N 0 -7.072 -0.333 -4.949
44 C56 C C43 N Y N 0 -7.182 -0.071 -3.586
45 C59 C C44 R N N 0 -4.324 2.588 0.873
46 C65 C C48 R N N 0 -0.702 3.533 1.68
47 C60 C C45 N N N 0 -4.96 3.66 -0.016
48 C61 C C46 N N N 0 -6.473 3.678 0.211
49 C62 C C47 N N N 0 -2.827 2.605 0.755
50 C66 C C49 N N N 0 -0.104 4.947 1.716
51 C67 C C50 N N N 0 -1.251 5.912 1.39
52 C68 C C51 N N N 0 -2.511 5.037 1.315
53 C69 C C52 N N N 0 0.117 2.684 0.761
54 C72 C C53 N N N 0 0.905 1.166 2.523
55 N10 N N1 N N N 0 3.318 6.951 -0.648
56 N13 N N2 N N N 0 1.885 -1.487 0.967
57 N29 N N3 N N N 0 8.208 -1.083 -2.739
58 N31 N N4 N N N 0 -0.75 -3.017 2.44
59 N48 N N5 N N N 0 -5.674 -1.18 -0.38
60 N49 N N6 N N N 0 -4.827 1.266 0.417
61 N52 N N7 N Y N 0 -5.494 -1.67 -3.143
62 N63 N N8 N N N 0 -2.087 3.644 1.195
63 N71 N N9 N N N 0 0.843 1.605 1.132
64 O42 O O5 N N N 0 -2.754 -1.04 2.327
65 O19 O O2 N N N 0 4.307 -3.479 -0.494
66 O32 O O3 N N N 0 1.287 -3.27 3.288
67 O41 O O4 N N N 0 -4.016 -2.608 1.374
68 O47 O O6 N N N 0 -4.611 0.575 2.519
69 O57 O O7 N N N 0 -8.068 0.849 -3.129
70 O58 O O8 N N N 0 -7.259 0.31 -0.827
71 O64 O O9 N N N 0 -2.264 1.653 0.239
72 O70 O O10 N N N 0 0.143 2.998 -0.417
73 S21 S S1 N N N 0 6.699 -2.375 0.447
74 H1 H H1 N N N 0 1.124 1.241 -0.881
75 H2 H H2 N N N 0 3.513 1.056 0.983
76 H3 H H3 N N N 0 3.538 0.837 -0.784
77 H4 H H4 N N N 0 3.079 3.234 1.959
78 H5 H H5 N N N 0 3.202 5.674 1.664
79 H6 H H6 N N N 0 3.273 5.147 -2.58
80 H7 H H7 N N N 0 3.145 2.708 -2.274
81 H8 H H8 N N N 0 4.365 8.002 0.835
82 H9 H H9 N N N 0 2.874 8.787 0.264
83 H10 H H10 N N N 0 2.779 7.369 1.335
84 H11 H H11 N N N 0 4.418 7.612 -2.307
85 H12 H H12 N N N 0 2.847 6.869 -2.69
86 H13 H H13 N N N 0 2.912 8.506 -1.995
87 H14 H H14 N N N 0 2.681 -1.586 2.894
88 H15 H H15 N N N 0 3.316 -0.245 1.945
89 H16 H H16 N N N 0 4.579 -2.671 2.345
90 H17 H H17 N N N 0 2.083 -4.515 -0.083
91 H18 H H18 N N N 0 2.44 -4.488 1.658
92 H19 H H19 N N N 0 0.548 -2.893 0.159
93 H20 H H20 N N N 0 4.883 -0.9 -0.122
94 H21 H H21 N N N 0 5.559 -0.523 1.481
95 H22 H H22 N N N 0 8.035 -0.373 0.349
96 H23 H H23 N N N 0 9.627 -2.292 0.346
97 H24 H H24 N N N 0 9.881 -3.602 -1.774
98 H25 H H25 N N N 0 8.243 -3.8 -1.1
99 H26 H H26 N N N 0 10.332 -0.095 -0.598
100 H27 H H27 N N N 0 11.101 -1.438 -1.481
101 H28 H H28 N N N 0 6.321 -1.173 -1.82
102 H29 H H29 N N N 0 7.189 0.367 -1.612
103 H30 H H30 N N N 0 8.995 -2.786 -3.687
104 H31 H H31 N N N 0 7.359 -2.985 -3.014
105 H32 H H32 N N N 0 9.399 0.635 -2.523
106 H33 H H33 N N N 0 10.166 -0.708 -3.405
107 H34 H H34 N N N 0 -1.055 -2.114 0.548
108 H35 H H35 N N N 0 -2.3 -5.073 2.436
109 H36 H H36 N N N 0 -2.909 -7.2 1.355
110 H37 H H37 N N N 0 -2.901 -7.379 -1.101
111 H38 H H38 N N N 0 -2.284 -5.431 -2.476
112 H39 H H39 N N N 0 -1.683 -3.302 -1.395
113 H40 H H40 N N N 0 -6.023 -2.965 1.561
114 H41 H H41 N N N 0 -4.632 -1.25 3.649
115 H42 H H42 N N N 0 -6.37 -1.63 3.601
116 H43 H H43 N N N 0 -5.179 -2.936 3.811
117 H44 H H44 N N N 0 -6.84 -0.76 1.293
118 H45 H H45 N N N 0 -4.653 -2.67 -4.751
119 H46 H H46 N N N 0 -6.045 -1.507 -6.417
120 H47 H H47 N N N 0 -7.689 0.192 -5.664
121 H48 H H48 N N N 0 -4.619 2.75 1.908
122 H49 H H49 N N N 0 -4.543 4.635 0.236
123 H50 H H50 N N N 0 -4.752 3.435 -1.062
124 H51 H H51 N N N 0 -6.926 4.442 -0.422
125 H52 H H52 N N N 0 -6.89 2.703 -0.041
126 H53 H H53 N N N 0 -6.681 3.903 1.257
127 H54 H H54 N N N 0 -0.726 3.133 2.691
128 H55 H H55 N N N 0 0.298 5.159 2.704
129 H56 H H56 N N N 0 0.681 5.032 0.966
130 H57 H H57 N N N 0 -1.355 6.661 2.17
131 H58 H H58 N N N 0 -1.074 6.392 0.427
132 H59 H H59 N N N 0 -3.113 5.179 2.206
133 H60 H H60 N N N 0 -3.075 5.339 0.431
134 H61 H H61 N N N 0 1.736 1.663 3.024
135 H62 H H62 N N N 0 -0.027 1.421 3.027
136 H63 H H63 N N N 0 1.053 0.087 2.557
137 H65 H H65 N N N 0 -1.163 -3.174 3.312
138 H66 H H66 N N N 0 -5.04 -1.835 -0.712
139 H67 H H67 N N N 0 -4.999 1.097 -0.521
140 H68 H H68 N N N 0 -8.942 0.487 -2.926



H8Q : Chemical Bonds

Total Number of Bonds: 147
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O57 C56 O C sing 1.36 N N
2 C55 C56 C C doub 1.39 N Y
3 C55 C54 C C sing 1.38 N Y
4 C56 C51 C C sing 1.4 N Y
5 C54 C53 C C doub 1.39 N Y
6 C51 C50 C C sing 1.48 N N
7 C51 N52 C N doub 1.33 N Y
8 C53 N52 C N sing 1.31 N Y
9 C44 C43 C C sing 1.52 N N
10 N48 C50 N C sing 1.35 N N
11 N48 C45 N C sing 1.47 N N
12 C50 O58 C O doub 1.22 N N
13 C45 C43 C C sing 1.52 N N
14 C45 C46 C C sing 1.5 N N
15 C43 O41 C O sing 1.43 N N
16 O47 C46 O C doub 1.21 N N
17 O42 C34 O C doub 1.21 N N
18 C46 N49 C N sing 1.37 N N
19 O41 C34 O C sing 1.33 N N
20 C34 C33 C C sing 1.52 N N
21 N49 C59 N C sing 1.49 N N
22 O32 C30 O C doub 1.22 N N
23 C60 C59 C C sing 1.53 N N
24 C60 C61 C C sing 1.53 N N
25 C59 C62 C C sing 1.5 N N
26 C33 N31 C N sing 1.47 N N
27 C33 C35 C C sing 1.51 N N
28 O19 C16 O C doub 1.21 N N
29 C30 N31 C N sing 1.36 N N
30 C30 C18 C C sing 1.5 N N
31 C36 C35 C C doub 1.38 N Y
32 C36 C37 C C sing 1.38 N Y
33 C17 C16 C C sing 1.51 N N
34 C17 C18 C C sing 1.53 N N
35 C35 C40 C C sing 1.38 N Y
36 C24 C23 C C sing 1.53 N N
37 C24 C27 C C sing 1.53 N N
38 C16 C15 C C sing 1.51 N N
39 C18 N13 C N sing 1.48 N N
40 C37 C38 C C doub 1.38 N Y
41 C62 O64 C O doub 1.22 N N
42 C62 N63 C N sing 1.35 N N
43 C23 C25 C C sing 1.53 N N
44 C23 C22 C C sing 1.53 N N
45 C27 N29 C N sing 1.47 N N
46 C11 N10 C N sing 1.47 N N
47 C6 C5 C C doub 1.38 N Y
48 C6 C7 C C sing 1.39 N Y
49 C40 C39 C C doub 1.38 N Y
50 C25 C28 C C sing 1.53 N N
51 C5 C4 C C sing 1.38 N Y
52 N63 C68 N C sing 1.46 N N
53 N63 C65 N C sing 1.47 N N
54 C15 C14 C C sing 1.53 N N
55 C15 C20 C C sing 1.53 N N
56 C38 C39 C C sing 1.38 N Y
57 S21 C22 S C sing 1.81 N N
58 S21 C20 S C sing 1.81 N N
59 N13 C14 N C sing 1.46 N N
60 N13 C1 N C sing 1.34 N N
61 C68 C67 C C sing 1.54 N N
62 N10 C7 N C sing 1.4 N N
63 N10 C12 N C sing 1.46 N N
64 C22 C26 C C sing 1.53 N N
65 C7 C8 C C doub 1.39 N Y
66 C28 N29 C N sing 1.47 N N
67 N29 C26 N C sing 1.47 N N
68 C65 C69 C C sing 1.5 N N
69 C65 C66 C C sing 1.54 N N
70 C2 C1 C C sing 1.49 N N
71 C2 C3 C C sing 1.52 N N
72 C2 N71 C N sing 1.47 N N
73 C4 C3 C C sing 1.51 N N
74 C4 C9 C C doub 1.38 N Y
75 C1 O1 C O doub 1.24 N N
76 C67 C66 C C sing 1.53 N N
77 C69 O70 C O doub 1.22 N N
78 C69 N71 C N sing 1.35 N N
79 N71 C72 N C sing 1.46 N N
80 C8 C9 C C sing 1.38 N Y
81 C2 H1 C H sing 1.12 N N
82 C3 H2 C H sing 1.09 N N
83 C3 H3 C H sing 1.09 N N
84 C5 H4 C H sing 1.08 N N
85 C6 H5 C H sing 1.08 N N
86 C8 H6 C H sing 1.08 N N
87 C9 H7 C H sing 1.08 N N
88 C11 H8 C H sing 1.09 N N
89 C11 H9 C H sing 1.09 N N
90 C11 H10 C H sing 1.09 N N
91 C12 H11 C H sing 1.09 N N
92 C12 H12 C H sing 1.09 N N
93 C12 H13 C H sing 1.09 N N
94 C14 H14 C H sing 1.1 N N
95 C14 H15 C H sing 1.08 N N
96 C15 H16 C H sing 1.09 N N
97 C17 H17 C H sing 1.09 N N
98 C17 H18 C H sing 1.09 N N
99 C18 H19 C H sing 1.08 N N
100 C20 H20 C H sing 1.09 N N
101 C20 H21 C H sing 1.09 N N
102 C22 H22 C H sing 1.09 N N
103 C23 H23 C H sing 1.09 N N
104 C24 H24 C H sing 1.09 N N
105 C24 H25 C H sing 1.09 N N
106 C25 H26 C H sing 1.09 N N
107 C25 H27 C H sing 1.09 N N
108 C26 H28 C H sing 1.09 N N
109 C26 H29 C H sing 1.09 N N
110 C27 H30 C H sing 1.09 N N
111 C27 H31 C H sing 1.09 N N
112 C28 H32 C H sing 1.09 N N
113 C28 H33 C H sing 1.09 N N
114 C33 H34 C H sing 1.08 N N
115 C36 H35 C H sing 1.08 N N
116 C37 H36 C H sing 1.08 N N
117 C38 H37 C H sing 1.08 N N
118 C39 H38 C H sing 1.08 N N
119 C40 H39 C H sing 1.08 N N
120 C43 H40 C H sing 1.12 N N
121 C44 H41 C H sing 1.09 N N
122 C44 H42 C H sing 1.09 N N
123 C44 H43 C H sing 1.09 N N
124 C45 H44 C H sing 1.1 N N
125 C53 H45 C H sing 1.08 N N
126 C54 H46 C H sing 1.08 N N
127 C55 H47 C H sing 1.08 N N
128 C59 H48 C H sing 1.09 N N
129 C60 H49 C H sing 1.09 N N
130 C60 H50 C H sing 1.09 N N
131 C61 H51 C H sing 1.09 N N
132 C61 H52 C H sing 1.09 N N
133 C61 H53 C H sing 1.09 N N
134 C65 H54 C H sing 1.09 N N
135 C66 H55 C H sing 1.09 N N
136 C66 H56 C H sing 1.09 N N
137 C67 H57 C H sing 1.09 N N
138 C67 H58 C H sing 1.09 N N
139 C68 H59 C H sing 1.08 N N
140 C68 H60 C H sing 1.09 N N
141 C72 H61 C H sing 1.09 N N
142 C72 H62 C H sing 1.09 N N
143 C72 H63 C H sing 1.09 N N
144 N31 H65 N H sing 0.98 N N
145 N48 H66 N H sing 0.97 N N
146 N49 H67 N H sing 0.97 N N
147 O57 H68 O H sing 0.97 N N



H8Q : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
H8Q 6zsa Open in New Window Bound ligand 1 1
H8Q 7og4 Open in New Window Bound ligand 1 1