Chemical Components in the PDB

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L88 : Summary

Code

L88

One-letter code

X

Molecule name

(4R,22R)-5,21-dioxo-4,22-bis({3-[4-(4-phenylthiophen-2-yl)phenyl]propanoyl}amino)-10,13,16-trioxa-6,20-diazapentacosane-1,25-dioic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 (4R,22R)-5,21-dioxo-4,22-bis({3-[4-(4-phenylthiophen-2-yl)phenyl]propanoyl}amino)-10,13,16-trioxa-6,20-diazapentacosane-1,25-dioic acid (non-preferred name)
OpenEye OEToolkits 1.7.6 (4R)-5-oxidanylidene-5-[3-[2-[2-[3-[[(2R)-5-oxidanyl-5-oxidanylidene-2-[3-[4-(4-phenylthiophen-2-yl)phenyl]propanoylamino]pentanoyl]amino]propoxy]ethoxy]ethoxy]propylamino]-4-[3-[4-(4-phenylthiophen-2-yl)phenyl]propanoylamino]pentanoic acid

Formula

C58 H66 N4 O11 S2

Formal charge

0

Molecular weight

1059.295 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)CCC(NC(=O)CCc3ccc(c2scc(c1ccccc1)c2)cc3)C(=O)NCCCOCCOCCOCCCNC(=O)C(NC(=O)CCc6ccc(c5scc(c4ccccc4)c5)cc6)CCC(=O)O
SMILES CACTVS 3.370 OC(=O)CC[CH](NC(=O)CCc1ccc(cc1)c2scc(c2)c3ccccc3)C(=O)NCCCOCCOCCOCCCNC(=O)[CH](CCC(O)=O)NC(=O)CCc4ccc(cc4)c5scc(c5)c6ccccc6
SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)c2cc(sc2)c3ccc(cc3)CCC(=O)NC(CCC(=O)O)C(=O)NCCCOCCOCCOCCCNC(=O)C(CCC(=O)O)NC(=O)CCc4ccc(cc4)c5cc(cs5)c6ccccc6
Canonical SMILES CACTVS 3.370 OC(=O)CC[C@@H](NC(=O)CCc1ccc(cc1)c2scc(c2)c3ccccc3)C(=O)NCCCOCCOCCOCCCNC(=O)[C@@H](CCC(O)=O)NC(=O)CCc4ccc(cc4)c5scc(c5)c6ccccc6
Canonical SMILES OpenEye OEToolkits 1.7.6 c1ccc(cc1)c2cc(sc2)c3ccc(cc3)CCC(=O)N[C@H](CCC(=O)O)C(=O)NCCCOCCOCCOCCCNC(=O)[C@@H](CCC(=O)O)NC(=O)CCc4ccc(cc4)c5cc(cs5)c6ccccc6

IUPAC InChI

InChI=1S/C58H66N4O11S2/c63-53(25-17-41-13-19-45(20-14-41)51-37-47(39-74-51)43-9-3-1-4-10-43)61-49(23-27-55(65)66)57(69)59-29-7-31-71-33-35-73-36-34-72-32-8-30-60-58(70)50(24-28-56(67)68)62-54(64)26-18-42-15-21-46(22-16-42)52-38-48(40-75-52)44-11-5-2-6-12-44/h1-6,9-16,19-22,37-40,49-50H,7-8,17-18,23-36H2,(H,59,69)(H,60,70)(H,61,63)(H,62,64)(H,65,66)(H,67,68)/t49-,50-/m1/s1

IUPAC InChI key

PAOWMYIFDMOPGM-CDKYPKJRSA-N
L88

wwPDB Information

Atom count

141 (75 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-11-20

Last modified at

2013-04-19

Status

Released

Obsoleted

Not Assigned



L88 : Atoms of Molecule

Total Number of Atoms: 141
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 -13.869 -9.478 -2.985
2 C10 C C10 N N N 0 9.67 3.835 -4.283
3 C11 C C11 N N N 0 8.878 0.73 -1.255
4 C12 C C12 N N N 0 9.862 -0.194 -0.585
5 C13 C C13 N N N 0 10.14 -1.391 -1.496
6 C14 C C14 N Y N 0 10.667 -3.334 -0.01
7 C15 C C15 N Y N 0 13.389 -2.98 -0.418
8 C16 C C16 N Y N 0 12.934 -4.011 0.406
9 C17 C C17 N Y N 0 11.563 -4.183 0.607
10 C18 C C18 N Y N 0 13.9 -4.917 1.064
11 C19 C C19 N Y N 0 15.237 -4.842 0.942
12 C2 C C2 N Y N 0 -15.003 -10.17 -3.371
13 C20 C C20 N Y N 0 15.939 -5.808 1.651
14 C21 C C21 N Y N 0 17.421 -5.89 1.642
15 C22 C C22 N Y N 0 18.167 -4.98 0.896
16 C23 C C23 N Y N 0 19.545 -5.057 0.897
17 C24 C C24 N Y N 0 20.185 -6.043 1.626
18 C25 C C25 N Y N 0 19.449 -6.953 2.363
19 C26 C C26 N Y N 0 18.071 -6.881 2.375
20 C27 C C27 N Y N 0 11.125 -2.314 -0.826
21 C28 C C28 N Y N 0 12.482 -2.142 -1.033
22 C29 C C29 N Y N 0 15.167 -6.665 2.349
23 C3 C C3 N Y N 0 -16.259 -9.678 -3.063
24 C4 C C4 N Y N 0 -16.386 -8.495 -2.363
25 C5 C C5 N N N 0 -10.748 -0.9 1.944
26 C53 C C53 N N N 0 5.162 5.247 0.397
27 C54 C C54 N N N 0 4.167 6.187 -0.286
28 C55 C C55 N N N 0 3.425 7.003 0.775
29 C57 C C57 N N N 0 1.747 8.693 1.043
30 C58 C C58 N N N 0 0.79 9.589 0.254
31 C6 C C6 N N N 0 6.803 3.565 -0.247
32 C68 C C68 N N N 0 -1.125 9.521 -1.186
33 C69 C C69 N N N 0 -2.107 8.557 -1.855
34 C7 C C7 R N N 0 7.534 2.762 -1.291
35 C71 C C71 N N N 0 -3.828 6.959 -1.374
36 C72 C C72 N N N 0 -4.589 6.307 -0.218
37 C73 C C73 N N N 0 -5.609 5.312 -0.776
38 C75 C C75 N N N 0 -7.293 3.771 0.076
39 C76 C C76 R N N 0 -8.043 3.129 1.215
40 C78 C C78 N N N 0 -8.77 4.207 2.02
41 C79 C C79 N N N 0 -10.145 4.634 4.039
42 C8 C C8 N N N 0 8.288 3.708 -2.228
43 C83 C C83 N N N 0 -9.429 3.571 3.246
44 C84 C C84 N N N 0 -9.44 1.145 1.439
45 C86 C C86 N N N 0 -10.444 0.165 0.889
46 C87 C C87 N Y N 0 -11.753 -1.88 1.395
47 C88 C C88 N Y N 0 -13.106 -1.647 1.565
48 C89 C C89 N Y N 0 -14.031 -2.54 1.064
49 C9 C C9 N N N 0 8.927 2.903 -3.361
50 C90 C C90 N Y N 0 -13.599 -3.68 0.384
51 C91 C C91 N Y N 0 -12.233 -3.908 0.215
52 C92 C C92 N Y N 0 -11.318 -3.005 0.716
53 C93 C C93 N Y N 0 -14.585 -4.641 -0.155
54 C94 C C94 N Y N 0 -14.281 -5.769 -0.82
55 C95 C C95 N Y N 0 -15.379 -6.515 -1.23
56 C96 C C96 N Y N 0 -16.573 -5.986 -0.896
57 C98 C C98 N Y N 0 -15.248 -7.791 -1.977
58 C99 C C99 N Y N 0 -13.985 -8.291 -2.29
59 H1 H H1 N N N 0 10.792 0.342 -0.396
60 H10 H H10 N N N 0 21.264 -6.102 1.619
61 H11 H H11 N N N 0 20.125 -4.348 0.324
62 H12 H H12 N N N 0 17.669 -4.209 0.327
63 H13 H H13 N N N 0 15.726 -4.094 0.335
64 H14 H H14 N N N 0 14.448 -2.844 -0.58
65 H15 H H15 N N N 0 12.833 -1.344 -1.671
66 H16 H H16 N N N 0 8.835 2.079 0.241
67 H17 H H17 N N N 0 6.817 2.177 -1.867
68 H18 H H18 N N N 0 7.592 4.436 -2.646
69 H19 H H19 N N N 0 9.065 4.229 -1.669
70 H2 H H2 N N N 0 9.446 -0.545 0.359
71 H20 H H20 N N N 0 9.623 2.176 -2.942
72 H21 H H21 N N N 0 8.15 2.382 -3.919
73 H22 H H22 N N N 0 10.775 3.984 -5.917
74 H23 H H23 N N N 0 5.672 4.596 -1.558
75 H24 H H24 N N N 0 4.625 4.573 1.064
76 H25 H H25 N N N 0 5.879 5.832 0.973
77 H26 H H26 N N N 0 4.704 6.862 -0.953
78 H27 H H27 N N N 0 3.45 5.602 -0.861
79 H28 H H28 N N N 0 2.888 6.329 1.442
80 H29 H H29 N N N 0 4.142 7.589 1.35
81 H3 H H3 N N N 0 9.21 -1.927 -1.686
82 H30 H H30 N N N 0 1.175 8.054 1.716
83 H31 H H31 N N N 0 2.429 9.314 1.624
84 H32 H H32 N N N 0 0.283 10.27 0.938
85 H33 H H33 N N N 0 1.353 10.164 -0.481
86 H34 H H34 N N N 0 -1.672 10.201 -0.532
87 H35 H H35 N N N 0 -0.602 10.095 -1.951
88 H36 H H36 N N N 0 -2.774 9.115 -2.512
89 H37 H H37 N N N 0 -1.553 7.821 -2.438
90 H38 H H38 N N N 0 -4.531 7.484 -2.021
91 H39 H H39 N N N 0 -3.31 6.191 -1.947
92 H4 H H4 N N N 0 10.556 -1.04 -2.441
93 H40 H H40 N N N 0 -3.887 5.782 0.429
94 H41 H H41 N N N 0 -5.107 7.075 0.356
95 H42 H H42 N N N 0 -6.312 5.837 -1.423
96 H43 H H43 N N N 0 -5.091 4.544 -1.35
97 H44 H H44 N N N 0 -6.133 4.933 1.246
98 H45 H H45 N N N 0 -7.34 2.604 1.862
99 H46 H H46 N N N 0 -8.055 4.964 2.343
100 H47 H H47 N N N 0 -9.535 4.672 1.397
101 H48 H H48 N N N 0 -10.144 2.815 2.923
102 H49 H H49 N N N 0 -8.664 3.106 3.869
103 H5 H H5 N N N 0 9.607 -3.466 0.144
104 H50 H H50 N N N 0 -11.243 5.021 5.639
105 H51 H H51 N N N 0 -9.364 2.289 -0.22
106 H52 H H52 N N N 0 -11.363 0.693 0.631
107 H53 H H53 N N N 0 -10.037 -0.312 -0.0020
108 H54 H H54 N N N 0 -9.83 -1.428 2.202
109 H55 H H55 N N N 0 -11.156 -0.423 2.835
110 H56 H H56 N N N 0 -13.439 -0.765 2.092
111 H57 H H57 N N N 0 -15.087 -2.358 1.199
112 H58 H H58 N N N 0 -11.892 -4.788 -0.31
113 H59 H H59 N N N 0 -10.26 -3.178 0.583
114 H6 H H6 N N N 0 11.205 -4.978 1.243
115 H60 H H60 N N N 0 -13.263 -6.073 -1.019
116 H61 H H61 N N N 0 -17.533 -6.422 -1.13
117 H62 H H62 N N N 0 -13.1 -7.751 -1.99
118 H63 H H63 N N N 0 -12.892 -9.867 -3.228
119 H64 H H64 N N N 0 -14.908 -11.099 -3.914
120 H65 H H65 N N N 0 -17.14 -10.222 -3.367
121 H66 H H66 N N N 0 -17.367 -8.114 -2.119
122 H7 H H7 N N N 0 15.534 -7.478 2.957
123 H8 H H8 N N N 0 17.497 -7.592 2.951
124 H9 H H9 N N N 0 19.954 -7.721 2.93
125 N1 N N1 N N N 0 5.872 4.466 -0.618
126 N2 N N2 N N N 0 8.486 1.861 -0.637
127 N74 N N74 N N N 0 -6.338 4.687 0.331
128 N82 N N82 N N N 0 -9.02 2.176 0.68
129 O1 O O1 N N N 0 7.054 3.402 0.929
130 O2 O O2 N N N 0 8.442 0.457 -2.354
131 O4 O O4 N N N 0 10.313 3.347 -5.355
132 O4E O O4E N N N 0 9.686 5.022 -4.057
133 O56 O O56 N N N 0 2.496 7.882 0.137
134 O67 O O67 N N N 0 -0.178 8.778 -0.416
135 O70 O O70 N N N 0 -2.875 7.888 -0.852
136 O77 O O77 N N N 0 -7.55 3.464 -1.069
137 O80 O O80 N N N 0 -10.13 5.782 3.663
138 O81 O O81 N N N 0 -10.799 4.305 5.164
139 O85 O O85 N N N 0 -9.009 1.004 2.564
140 S7 S S7 N Y N 0 13.472 -6.257 2.118
141 S97 S S97 N Y N 0 -16.33 -4.483 -0.017



L88 : Chemical Bonds

Total Number of Bonds: 146
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C29 S7 C S sing 1.76 N Y
2 C29 C20 C C doub 1.35 N Y
3 S7 C18 S C sing 1.76 N Y
4 C22 C23 C C doub 1.38 N Y
5 C22 C21 C C sing 1.39 N Y
6 C23 C24 C C sing 1.38 N Y
7 C20 C21 C C sing 1.48 N N
8 C20 C19 C C sing 1.39 N Y
9 C21 C26 C C doub 1.39 N Y
10 C15 C28 C C doub 1.38 N Y
11 C15 C16 C C sing 1.4 N Y
12 C18 C19 C C doub 1.34 N Y
13 C18 C16 C C sing 1.48 N N
14 C24 C25 C C doub 1.38 N Y
15 C28 C27 C C sing 1.38 N Y
16 C16 C17 C C doub 1.4 N Y
17 C26 C25 C C sing 1.38 N Y
18 C27 C13 C C sing 1.51 N N
19 C27 C14 C C doub 1.38 N Y
20 C17 C14 C C sing 1.38 N Y
21 C13 C12 C C sing 1.53 N N
22 C12 C11 C C sing 1.51 N N
23 O2 C11 O C doub 1.21 N N
24 O4E C10 O C doub 1.21 N N
25 C11 N2 C N sing 1.35 N N
26 C10 C9 C C sing 1.51 N N
27 C10 O4 C O sing 1.34 N N
28 N2 C7 N C sing 1.46 N N
29 C9 C8 C C sing 1.53 N N
30 C8 C7 C C sing 1.53 N N
31 C7 C6 C C sing 1.51 N N
32 N1 C6 N C sing 1.35 N N
33 N1 C53 N C sing 1.46 N N
34 C6 O1 C O doub 1.21 N N
35 C53 C54 C C sing 1.53 N N
36 C54 C55 C C sing 1.53 N N
37 C68 C69 C C sing 1.53 N N
38 C68 O67 C O sing 1.43 N N
39 C69 O70 C O sing 1.43 N N
40 C58 O67 C O sing 1.43 N N
41 C58 C57 C C sing 1.53 N N
42 C55 O56 C O sing 1.43 N N
43 C71 O70 C O sing 1.43 N N
44 C71 C72 C C sing 1.53 N N
45 O56 C57 O C sing 1.43 N N
46 C72 C73 C C sing 1.53 N N
47 C73 N74 C N sing 1.47 N N
48 O77 C75 O C doub 1.21 N N
49 N74 C75 N C sing 1.35 N N
50 C75 C76 C C sing 1.51 N N
51 C76 C78 C C sing 1.53 N N
52 C76 N82 C N sing 1.47 N N
53 C78 C83 C C sing 1.53 N N
54 O80 C79 O C doub 1.21 N N
55 C83 C79 C C sing 1.51 N N
56 N82 C84 N C sing 1.35 N N
57 C79 O81 C O sing 1.34 N N
58 C84 O85 C O doub 1.21 N N
59 C84 C86 C C sing 1.51 N N
60 C86 C5 C C sing 1.53 N N
61 C88 C89 C C doub 1.38 N Y
62 C88 C87 C C sing 1.38 N Y
63 C5 C87 C C sing 1.51 N N
64 C89 C90 C C sing 1.4 N Y
65 C87 C92 C C doub 1.38 N Y
66 C1 C99 C C doub 1.38 N Y
67 C1 C2 C C sing 1.38 N Y
68 C99 C98 C C sing 1.39 N Y
69 C90 C93 C C sing 1.48 N N
70 C90 C91 C C doub 1.4 N Y
71 C92 C91 C C sing 1.38 N Y
72 C2 C3 C C doub 1.38 N Y
73 C94 C93 C C doub 1.34 N Y
74 C94 C95 C C sing 1.39 N Y
75 C93 S97 C S sing 1.76 N Y
76 C98 C95 C C sing 1.48 N N
77 C98 C4 C C doub 1.39 N Y
78 C95 C96 C C doub 1.35 N Y
79 C3 C4 C C sing 1.38 N Y
80 S97 C96 S C sing 1.76 N Y
81 C12 H1 C H sing 1.09 N N
82 C12 H2 C H sing 1.09 N N
83 C13 H3 C H sing 1.09 N N
84 C13 H4 C H sing 1.09 N N
85 C14 H5 C H sing 1.08 N N
86 C17 H6 C H sing 1.08 N N
87 C29 H7 C H sing 1.08 N N
88 C26 H8 C H sing 1.08 N N
89 C25 H9 C H sing 1.08 N N
90 C24 H10 C H sing 1.08 N N
91 C23 H11 C H sing 1.08 N N
92 C22 H12 C H sing 1.08 N N
93 C19 H13 C H sing 1.08 N N
94 C15 H14 C H sing 1.08 N N
95 C28 H15 C H sing 1.08 N N
96 N2 H16 N H sing 0.97 N N
97 C7 H17 C H sing 1.09 N N
98 C8 H18 C H sing 1.09 N N
99 C8 H19 C H sing 1.09 N N
100 C9 H20 C H sing 1.09 N N
101 C9 H21 C H sing 1.09 N N
102 O4 H22 O H sing 0.97 N N
103 N1 H23 N H sing 0.97 N N
104 C53 H24 C H sing 1.09 N N
105 C53 H25 C H sing 1.09 N N
106 C54 H26 C H sing 1.09 N N
107 C54 H27 C H sing 1.09 N N
108 C55 H28 C H sing 1.09 N N
109 C55 H29 C H sing 1.09 N N
110 C57 H30 C H sing 1.09 N N
111 C57 H31 C H sing 1.09 N N
112 C58 H32 C H sing 1.09 N N
113 C58 H33 C H sing 1.09 N N
114 C68 H34 C H sing 1.09 N N
115 C68 H35 C H sing 1.09 N N
116 C69 H36 C H sing 1.09 N N
117 C69 H37 C H sing 1.09 N N
118 C71 H38 C H sing 1.09 N N
119 C71 H39 C H sing 1.09 N N
120 C72 H40 C H sing 1.09 N N
121 C72 H41 C H sing 1.09 N N
122 C73 H42 C H sing 1.09 N N
123 C73 H43 C H sing 1.09 N N
124 N74 H44 N H sing 0.97 N N
125 C76 H45 C H sing 1.09 N N
126 C78 H46 C H sing 1.09 N N
127 C78 H47 C H sing 1.09 N N
128 C83 H48 C H sing 1.09 N N
129 C83 H49 C H sing 1.09 N N
130 O81 H50 O H sing 0.97 N N
131 N82 H51 N H sing 0.97 N N
132 C86 H52 C H sing 1.09 N N
133 C86 H53 C H sing 1.09 N N
134 C5 H54 C H sing 1.09 N N
135 C5 H55 C H sing 1.09 N N
136 C88 H56 C H sing 1.08 N N
137 C89 H57 C H sing 1.08 N N
138 C91 H58 C H sing 1.08 N N
139 C92 H59 C H sing 1.08 N N
140 C94 H60 C H sing 1.08 N N
141 C96 H61 C H sing 1.08 N N
142 C99 H62 C H sing 1.08 N N
143 C1 H63 C H sing 1.08 N N
144 C2 H64 C H sing 1.08 N N
145 C3 H65 C H sing 1.08 N N
146 C4 H66 C H sing 1.08 N N



L88 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
L88 4i03 Open in New Window Bound ligand 1 1