Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

5BG : Summary

Code

5BG

One-letter code

X

Molecule name

{3-[(1R)-1-[({(2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)acetyl]piperidin-2-yl}carbonyl)amino]-3-(3,4-dimethoxyphenyl)propyl]phenoxy}acetic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 {3-[(1R)-1-[({(2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)acetyl]piperidin-2-yl}carbonyl)amino]-3-(3,4-dimethoxyphenyl)propyl]phenoxy}acetic acid
OpenEye OEToolkits 1.9.2 2-[3-[(1R)-1-[[(2S)-1-[(2S)-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidin-2-yl]carbonylamino]-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid

Formula

C42 H54 N2 O10

Formal charge

0

Molecular weight

746.886 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 COc1c(OC)c(OC)cc(c1)C(C2CCCCC2)C(N3CCCCC3C(=O)NC(CCc4ccc(OC)c(c4)OC)c5cccc(c5)OCC(=O)O)=O
SMILES CACTVS 3.385 COc1ccc(CC[CH](NC(=O)[CH]2CCCCN2C(=O)[CH](C3CCCCC3)c4cc(OC)c(OC)c(OC)c4)c5cccc(OCC(O)=O)c5)cc1OC
SMILES OpenEye OEToolkits 1.9.2 COc1ccc(cc1OC)CCC(c2cccc(c2)OCC(=O)O)NC(=O)C3CCCCN3C(=O)C(c4cc(c(c(c4)OC)OC)OC)C5CCCCC5
Canonical SMILES CACTVS 3.385 COc1ccc(CC[C@@H](NC(=O)[C@@H]2CCCCN2C(=O)[C@@H](C3CCCCC3)c4cc(OC)c(OC)c(OC)c4)c5cccc(OCC(O)=O)c5)cc1OC
Canonical SMILES OpenEye OEToolkits 1.9.2 COc1ccc(cc1OC)CC[C@H](c2cccc(c2)OCC(=O)O)NC(=O)[C@@H]3CCCCN3C(=O)[C@H](c4cc(c(c(c4)OC)OC)OC)C5CCCCC5

IUPAC InChI

InChI=1S/C42H54N2O10/c1-49-34-20-18-27(22-35(34)50-2)17-19-32(29-14-11-15-31(23-29)54-26-38(45)46)43-41(47)33-16-9-10-21-44(33)42(48)39(28-12-7-6-8-13-28)30-24-36(51-3)40(53-5)37(25-30)52-4/h11,14-15,18,20,22-25,28,32-33,39H,6-10,12-13,16-17,19,21,26H2,1-5H3,(H,43,47)(H,45,46)/t32-,33+,39+/m1/s1

IUPAC InChI key

HVSNNDISDMAIJE-XEAFTEEUSA-N
5BG

wwPDB Information

Atom count

108 (54 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-09-02

Last modified at

2016-03-18

Status

Released

Obsoleted

Not Assigned



5BG : Atoms of Molecule

Total Number of Atoms: 108
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAC C C1 N N N 0 -7.335 3.551 -0.727
2 OBH O O1 N N N 0 -7.303 2.727 0.44
3 CBU C C2 N Y N 0 -6.248 1.879 0.568
4 CAQ C C3 N Y N 0 -5.262 1.845 -0.407
5 CBW C C4 N Y N 0 -6.154 1.048 1.678
6 OBJ O O2 N N N 0 -7.117 1.082 2.639
7 CAE C C5 N N N 0 -8.226 0.196 2.478
8 CBV C C6 N Y N 0 -5.074 0.183 1.804
9 OBI O O3 N N N 0 -4.977 -0.632 2.889
10 CAD C C7 N N N 0 -3.84 -1.495 2.952
11 CAR C C8 N Y N 0 -4.095 0.151 0.823
12 CBR C C9 N Y N 0 -4.189 0.983 -0.278
13 CCA C C10 S N N 0 -3.12 0.949 -1.339
14 CBY C C11 N N N 0 -3.043 -0.455 -1.941
15 CAY C C12 N N N 0 -4.43 -0.877 -2.43
16 CAT C C13 N N N 0 -4.353 -2.282 -3.032
17 CAS C C14 N N N 0 -3.377 -2.279 -4.21
18 CAU C C15 N N N 0 -1.99 -1.856 -3.721
19 CAZ C C16 N N N 0 -2.067 -0.452 -3.119
20 CBN C C17 N N N 0 -1.791 1.306 -0.725
21 OAH O O4 N N N 0 -1.058 0.431 -0.316
22 N N N1 N N N 0 -1.418 2.598 -0.629
23 CBD C C18 N N N 0 -2.326 3.673 -1.052
24 CAW C C19 N N N 0 -2.484 4.667 0.102
25 CAV C C20 N N N 0 -1.102 5.151 0.547
26 CB C C21 N N N 0 -0.279 3.96 1.044
27 CA C C22 S N N 0 -0.098 2.958 -0.094
28 C C C23 N N N 0 0.592 1.723 0.425
29 O O O5 N N N 0 0.12 1.112 1.36
30 NBE N N2 N N N 0 1.735 1.298 -0.149
31 CBX C C24 R N N 0 2.407 0.098 0.356
32 CBQ C C25 N Y N 0 1.8 -1.124 -0.285
33 CAP C C26 N Y N 0 1.581 -2.261 0.468
34 CAL C C27 N Y N 0 1.459 -1.104 -1.624
35 CAJ C C28 N Y N 0 0.901 -2.223 -2.215
36 CAK C C29 N Y N 0 0.684 -3.364 -1.468
37 CBP C C30 N Y N 0 1.022 -3.385 -0.122
38 OBK O O6 N N N 0 0.806 -4.506 0.616
39 CBC C C31 N N N 0 0.228 -5.625 -0.058
40 CBL C C32 N N N 0 0.064 -6.766 0.913
41 OAI O O7 N N N 0 -0.464 -7.929 0.5
42 OAF O O8 N N N 0 0.407 -6.634 2.064
43 CBA C C33 N N N 0 3.897 0.166 0.016
44 CAX C C34 N N N 0 4.538 1.334 0.767
45 CBO C C35 N Y N 0 6.006 1.401 0.432
46 CAO C C36 N Y N 0 6.921 0.701 1.197
47 CAM C C37 N Y N 0 6.435 2.157 -0.643
48 CAN C C38 N Y N 0 7.78 2.221 -0.955
49 CBS C C39 N Y N 0 8.703 1.527 -0.189
50 OBF O O9 N N N 0 10.026 1.59 -0.494
51 CAA C C40 N N N 0 10.396 2.39 -1.618
52 CBT C C41 N Y N 0 8.27 0.757 0.887
53 OBG O O10 N N N 0 9.172 0.074 1.642
54 H5 H H5 N N N 0 -7.868 -0.834 2.458
55 CAB C C42 N N N 0 8.656 -0.695 2.73
56 H1 H H1 N N N 0 -6.447 4.183 -0.751
57 H2 H H2 N N N 0 -7.357 2.921 -1.617
58 H3 H H3 N N N 0 -8.226 4.179 -0.705
59 H4 H H4 N N N 0 -5.333 2.493 -1.268
60 H6 H H6 N N N 0 -8.918 0.324 3.311
61 H7 H H7 N N N 0 -8.738 0.421 1.542
62 H8 H H8 N N N 0 -2.929 -0.897 2.954
63 H9 H H9 N N N 0 -3.885 -2.089 3.865
64 H10 H H10 N N N 0 -3.838 -2.158 2.087
65 H11 H H11 N N N 0 -3.255 -0.521 0.92
66 H12 H H12 N N N 0 -3.363 1.668 -2.122
67 H13 H H13 N N N 0 -2.696 -1.157 -1.183
68 H14 H H14 N N N 0 -5.126 -0.88 -1.59
69 H15 H H15 N N N 0 -4.778 -0.176 -3.188
70 H16 H H16 N N N 0 -4.006 -2.984 -2.274
71 H17 H H17 N N N 0 -5.341 -2.583 -3.38
72 H18 H H18 N N N 0 -3.322 -3.279 -4.639
73 H19 H H19 N N N 0 -3.724 -1.577 -4.968
74 H20 H H20 N N N 0 -1.642 -2.558 -2.963
75 H21 H H21 N N N 0 -1.294 -1.854 -4.56
76 H22 H H22 N N N 0 -2.414 0.25 -3.877
77 H23 H H23 N N N 0 -1.079 -0.151 -2.771
78 H24 H H24 N N N 0 -1.908 4.183 -1.92
79 H25 H H25 N N N 0 -3.297 3.25 -1.309
80 H26 H H26 N N N 0 -3.078 5.519 -0.231
81 H27 H H27 N N N 0 -2.985 4.179 0.937
82 H28 H H28 N N N 0 -0.592 5.618 -0.296
83 H29 H H29 N N N 0 -1.213 5.877 1.352
84 H30 H H30 N N N 0 0.697 4.306 1.383
85 H31 H H31 N N N 0 -0.803 3.481 1.871
86 H32 H H32 N N N 0 0.501 3.408 -0.886
87 H33 H H33 N N N 0 2.114 1.787 -0.896
88 H34 H H34 N N N 0 2.283 0.04 1.438
89 H36 H H36 N N N 0 1.627 -0.212 -2.21
90 H35 H H35 N N N 0 1.844 -2.275 1.515
91 H37 H H37 N N N 0 0.635 -2.204 -3.261
92 H38 H H38 N N N 0 0.248 -4.238 -1.929
93 H39 H H39 N N N 0 -0.747 -5.345 -0.457
94 H40 H H40 N N N 0 0.88 -5.934 -0.874
95 H41 H H41 N N N 0 -0.549 -8.631 1.158
96 H42 H H42 N N N 0 4.38 -0.766 0.312
97 H46 H H46 N N N 0 6.584 0.112 2.036
98 H43 H H43 N N N 0 4.018 0.313 -1.057
99 H44 H H44 N N N 0 4.056 2.266 0.47
100 H45 H H45 N N N 0 4.417 1.187 1.84
101 H47 H H47 N N N 0 5.717 2.699 -1.241
102 H48 H H48 N N N 0 8.112 2.812 -1.796
103 H49 H H49 N N N 0 9.907 2.007 -2.514
104 H50 H H50 N N N 0 10.086 3.421 -1.447
105 H51 H H51 N N N 0 11.477 2.353 -1.75
106 H52 H H52 N N N 0 9.478 -1.188 3.248
107 H53 H H53 N N N 0 8.131 -0.038 3.423
108 H54 H H54 N N N 0 7.965 -1.447 2.348



5BG : Chemical Bonds

Total Number of Bonds: 112
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAU CAS C C sing 1.53 N N
2 CAU CAZ C C sing 1.53 N N
3 CAS CAT C C sing 1.53 N N
4 CAZ CBY C C sing 1.53 N N
5 CAT CAY C C sing 1.53 N N
6 CBY CAY C C sing 1.53 N N
7 CBY CCA C C sing 1.53 N N
8 OAH CBN O C doub 1.21 N N
9 CBN CCA C C sing 1.51 N N
10 CBN N C N sing 1.35 N N
11 CB CA C C sing 1.53 N N
12 CB CAV C C sing 1.53 N N
13 CCA CBR C C sing 1.51 N N
14 CA N C N sing 1.47 N N
15 CA C C C sing 1.51 N N
16 N CBD N C sing 1.47 N N
17 CAB OBG C O sing 1.43 N N
18 CAV CAW C C sing 1.53 N N
19 CAW CBD C C sing 1.53 N N
20 C O C O doub 1.21 N N
21 C NBE C N sing 1.35 N N
22 OBG CBT O C sing 1.36 N N
23 CBR CAQ C C doub 1.38 N Y
24 CBR CAR C C sing 1.38 N Y
25 CAQ CBU C C sing 1.39 N Y
26 NBE CBX N C sing 1.47 N N
27 CAC OBH C O sing 1.43 N N
28 OBF CAA O C sing 1.43 N N
29 OBF CBS O C sing 1.36 N N
30 CAR CBV C C doub 1.39 N Y
31 CBT CBS C C doub 1.39 N Y
32 CBT CAO C C sing 1.39 N Y
33 CBS CAN C C sing 1.39 N Y
34 CBU OBH C O sing 1.36 N N
35 CBU CBW C C doub 1.39 N Y
36 CAO CBO C C doub 1.38 N Y
37 CBX CBA C C sing 1.53 N N
38 CBX CBQ C C sing 1.51 N N
39 CBA CAX C C sing 1.53 N N
40 CBV CBW C C sing 1.39 N Y
41 CBV OBI C O sing 1.36 N N
42 CBW OBJ C O sing 1.36 N N
43 CAN CAM C C doub 1.38 N Y
44 CBO CAM C C sing 1.38 N Y
45 CBO CAX C C sing 1.51 N N
46 CBQ CAL C C doub 1.38 N Y
47 CBQ CAP C C sing 1.38 N Y
48 CAD OBI C O sing 1.43 N N
49 CAL CAJ C C sing 1.38 N Y
50 CAP CBP C C doub 1.39 N Y
51 OBJ CAE O C sing 1.43 N N
52 CAJ CAK C C doub 1.38 N Y
53 CBP CAK C C sing 1.39 N Y
54 CBP OBK C O sing 1.36 N N
55 OBK CBC O C sing 1.43 N N
56 CBC CBL C C sing 1.51 N N
57 CBL OAF C O doub 1.21 N N
58 CBL OAI C O sing 1.34 N N
59 CAC H1 C H sing 1.09 N N
60 CAC H2 C H sing 1.09 N N
61 CAC H3 C H sing 1.09 N N
62 CAQ H4 C H sing 1.08 N N
63 CAE H5 C H sing 1.09 N N
64 CAE H6 C H sing 1.09 N N
65 CAE H7 C H sing 1.09 N N
66 CAD H8 C H sing 1.09 N N
67 CAD H9 C H sing 1.09 N N
68 CAD H10 C H sing 1.09 N N
69 CAR H11 C H sing 1.08 N N
70 CCA H12 C H sing 1.09 N N
71 CBY H13 C H sing 1.09 N N
72 CAY H14 C H sing 1.09 N N
73 CAY H15 C H sing 1.09 N N
74 CAT H16 C H sing 1.09 N N
75 CAT H17 C H sing 1.09 N N
76 CAS H18 C H sing 1.09 N N
77 CAS H19 C H sing 1.09 N N
78 CAU H20 C H sing 1.09 N N
79 CAU H21 C H sing 1.09 N N
80 CAZ H22 C H sing 1.09 N N
81 CAZ H23 C H sing 1.09 N N
82 CBD H24 C H sing 1.09 N N
83 CBD H25 C H sing 1.09 N N
84 CAW H26 C H sing 1.09 N N
85 CAW H27 C H sing 1.09 N N
86 CAV H28 C H sing 1.09 N N
87 CAV H29 C H sing 1.09 N N
88 CB H30 C H sing 1.09 N N
89 CB H31 C H sing 1.09 N N
90 CA H32 C H sing 1.09 N N
91 NBE H33 N H sing 0.97 N N
92 CBX H34 C H sing 1.09 N N
93 CAP H35 C H sing 1.08 N N
94 CAL H36 C H sing 1.08 N N
95 CAJ H37 C H sing 1.08 N N
96 CAK H38 C H sing 1.08 N N
97 CBC H39 C H sing 1.09 N N
98 CBC H40 C H sing 1.09 N N
99 OAI H41 O H sing 0.97 N N
100 CBA H42 C H sing 1.09 N N
101 CBA H43 C H sing 1.09 N N
102 CAX H44 C H sing 1.09 N N
103 CAX H45 C H sing 1.09 N N
104 CAO H46 C H sing 1.08 N N
105 CAM H47 C H sing 1.08 N N
106 CAN H48 C H sing 1.08 N N
107 CAA H49 C H sing 1.09 N N
108 CAA H50 C H sing 1.09 N N
109 CAA H51 C H sing 1.09 N N
110 CAB H52 C H sing 1.09 N N
111 CAB H53 C H sing 1.09 N N
112 CAB H54 C H sing 1.09 N N



5BG : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5BG 5diu Open in New Window Bound ligand 1 1