Chemical Components in the PDB

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0E9 : Summary

Code

0E9

One-letter code

X

Molecule name

benzyl [(1R,4S,6S,9R)-4,6-dibenzyl-5-hydroxy-1,9-bis(1-methylethyl)-2,8,11-trioxo-13-phenyl-12-oxa-3,7,10-triazatridec-1-yl]carbamate

Systematic names

ProgramVersionName
ACDLabs 10.04 benzyl [(1R,4S,6S,9R)-4,6-dibenzyl-5-hydroxy-1,9-bis(1-methylethyl)-2,8,11-trioxo-13-phenyl-12-oxa-3,7,10-triazatridec-1-yl]carbamate (non-preferred name)
OpenEye OEToolkits 1.6.1 phenylmethyl N-[(2S)-1-[[(2S,4S)-3-hydroxy-4-[[(2S)-3-methyl-2-phenylmethoxycarbonylamino-butanoyl]amino]-1,5-diphenyl-pentan-2-yl]amino]-3-methyl-1-oxo-butan-2-yl]carbamate

Formula

C43 H52 N4 O7

Formal charge

0

Molecular weight

736.896 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(OCc1ccccc1)NC(C(=O)NC(Cc2ccccc2)C(O)C(NC(=O)C(NC(=O)OCc3ccccc3)C(C)C)Cc4ccccc4)C(C)C
SMILES CACTVS 3.352 CC(C)[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](Cc2ccccc2)[CH](O)[CH](Cc3ccccc3)NC(=O)[CH](NC(=O)OCc4ccccc4)C(C)C
Canonical SMILES CACTVS 3.352 CC(C)[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](Cc2ccccc2)[C@@H](O)[C@H](Cc3ccccc3)NC(=O)[C@@H](NC(=O)OCc4ccccc4)C(C)C

IUPAC InChI

InChI=1S/C43H52N4O7/c1-29(2)37(46-42(51)53-27-33-21-13-7-14-22-33)40(49)44-35(25-31-17-9-5-10-18-31)39(48)36(26-32-19-11-6-12-20-32)45-41(50)38(30(3)4)47-43(52)54-28-34-23-15-8-16-24-34/h5-24,29-30,35-39,48H,25-28H2,1-4H3,(H,44,49)(H,45,50)(H,46,51)(H,47,52)/t35-,36-,37-,38-/m0/s1

IUPAC InChI key

GEANBHANAKKWSL-ZQWQDMLBSA-N
0E9

wwPDB Information

Atom count

106 (54 without Hydrogen)

Polymer type

Bound ligand

Type description

peptide-like

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2008-11-07

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



0E9 : Atoms of Molecule

Total Number of Atoms: 106
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -7.058 -0.798 0.377
2 O1 O O1 N N N 0 -7.511 -0.465 1.454
3 O2 O O2 N N N 0 -7.888 -1.055 -0.652
4 C2 C C2 N N N 0 -9.311 -0.914 -0.401
5 C3 C C3 N Y N 0 -10.077 -1.24 -1.658
6 C4 C C4 N Y N 0 -10.483 -2.538 -1.903
7 C5 C C5 N Y N 0 -11.186 -2.837 -3.055
8 C6 C C6 N Y N 0 -11.482 -1.837 -3.963
9 C7 C C7 N Y N 0 -11.077 -0.539 -3.717
10 C8 C C8 N Y N 0 -10.378 -0.239 -2.563
11 N N N1 N N N 0 -5.725 -0.904 0.209
12 CA C C9 S N N 0 -4.821 -0.618 1.327
13 C C C10 N N N 0 -3.474 -0.206 0.791
14 O O O3 N N N 0 -3.153 -0.508 -0.338
15 CB C C11 N N N 0 -4.665 -1.872 2.19
16 CG1 C C12 N N N 0 -3.777 -1.555 3.394
17 CG2 C C13 N N N 0 -6.041 -2.33 2.678
18 C11 C C14 N N N 0 -1.006 2.326 1.67
19 C21 C C15 S N N 0 -1.364 0.991 1.013
20 N2 N N2 N N N 0 -2.627 0.497 1.568
21 C31 C C16 N N N 0 -0.254 -0.026 1.288
22 O3 O O5 N N N 0 -0.615 -1.288 0.724
23 C41 C C17 S N N 0 1.051 0.461 0.656
24 N4 N N3 N N N 0 2.136 -0.458 1.007
25 C51 C C18 N N N 0 0.895 0.508 -0.865
26 C1A C C19 N Y N 0 -2.037 3.361 1.297
27 C2A C C20 N Y N 0 -3.157 3.536 2.088
28 C3A C C21 N Y N 0 -4.102 4.485 1.746
29 C4A C C22 N Y N 0 -3.927 5.259 0.614
30 C5A C C23 N Y N 0 -2.806 5.084 -0.176
31 C6A C C24 N Y N 0 -1.859 4.138 0.168
32 C1B C C25 N Y N 0 2.144 1.084 -1.481
33 C2B C C26 N Y N 0 3.183 0.248 -1.845
34 C3B C C27 N Y N 0 4.329 0.776 -2.41
35 C4B C C28 N Y N 0 4.436 2.14 -2.611
36 C5B C C29 N Y N 0 3.396 2.975 -2.247
37 C6B C C30 N Y N 0 2.249 2.447 -1.686
38 N1 N N4 N N N 0 5.764 -0.495 0.658
39 CA1 C C31 S N N 0 4.536 -0.99 1.285
40 C9 C C32 N N N 0 3.412 -0.023 1.019
41 O4 O O6 N N N 0 3.654 1.148 0.816
42 CB1 C C33 N N N 0 4.75 -1.121 2.794
43 CG11 C C34 N N N 0 3.49 -1.699 3.44
44 CG21 C C35 N N N 0 5.934 -2.053 3.062
45 C12 C C36 N N N 0 6.74 -1.359 0.314
46 O11 O O8 N N N 0 6.602 -2.547 0.524
47 O21 O O9 N N N 0 7.869 -0.904 -0.262
48 C22 C C37 N N N 0 8.878 -1.89 -0.605
49 C32 C C38 N Y N 0 10.061 -1.201 -1.235
50 C42 C C39 N Y N 0 11.101 -0.753 -0.443
51 C52 C C40 N Y N 0 12.186 -0.12 -1.02
52 C61 C C41 N Y N 0 12.231 0.063 -2.39
53 C71 C C42 N Y N 0 11.191 -0.386 -3.182
54 C81 C C43 N Y N 0 10.108 -1.023 -2.605
55 H21 H H2 N N N 0 -9.609 -1.598 0.393
56 H22 H H3 N N N 0 -9.528 0.111 -0.099
57 H41 H H4 N N N 0 -10.252 -3.319 -1.194
58 H51 H H5 N N N 0 -11.502 -3.852 -3.247
59 H61 H H6 N N N 0 -12.03 -2.071 -4.864
60 H71 H H7 N N N 0 -11.308 0.242 -4.427
61 H81 H H8 N N N 0 -10.064 0.776 -2.369
62 H H H9 N N N 0 -5.363 -1.169 -0.651
63 HA H H11 N N N 0 -5.235 0.189 1.931
64 HB H H12 N N N 0 -4.207 -2.665 1.599
65 HG11 H H13 N N N 0 -4.238 -0.766 3.988
66 HG12 H H14 N N N 0 -3.661 -2.45 4.006
67 HG13 H H15 N N N 0 -2.798 -1.224 3.046
68 HG21 H H16 N N N 0 -6.674 -2.556 1.819
69 HG22 H H17 N N N 0 -5.93 -3.224 3.292
70 HG23 H H18 N N N 0 -6.5 -1.537 3.269
71 H11 H H20 N N N 0 -0.988 2.205 2.753
72 H12 H H21 N N N 0 -0.025 2.65 1.323
73 H2 H H22 N N N 0 -1.47 1.132 -0.062
74 HN22 H H24 N N N 0 -2.853 0.677 2.494
75 H3 H H25 N N N 0 -0.119 -0.134 2.364
76 HO3 H H26 N N N 0 -0.752 -1.267 -0.233
77 H4 H H27 N N N 0 1.285 1.458 1.028
78 HN42 H H29 N N N 0 1.937 -1.381 1.231
79 H511 H H30 N N N 0 0.734 -0.501 -1.245
80 H52 H H31 N N N 0 0.041 1.134 -1.123
81 H2A H H32 N N N 0 -3.294 2.932 2.972
82 H6A H H36 N N N 0 -0.982 4.004 -0.447
83 H3A H H33 N N N 0 -4.978 4.622 2.364
84 H4A H H34 N N N 0 -4.666 6.0 0.347
85 H5A H H35 N N N 0 -2.67 5.689 -1.06
86 H2B H H37 N N N 0 3.1 -0.817 -1.688
87 H3B H H38 N N N 0 5.141 0.123 -2.694
88 H4B H H39 N N N 0 5.331 2.552 -3.052
89 H5B H H40 N N N 0 3.48 4.04 -2.404
90 H6B H H41 N N N 0 1.435 3.099 -1.406
91 H1 H H42 N N N 0 5.875 0.454 0.491
92 HA1 H H44 N N N 0 4.283 -1.965 0.868
93 HG16 H H48 N N N 0 2.672 -0.985 3.344
94 HB1 H H45 N N N 0 4.958 -0.139 3.218
95 HG14 H H46 N N N 0 3.22 -2.63 2.941
96 HG15 H H47 N N N 0 3.679 -1.895 4.496
97 HG24 H H49 N N N 0 6.832 -1.64 2.602
98 HG25 H H50 N N N 0 6.087 -2.146 4.137
99 HG26 H H51 N N N 0 5.727 -3.035 2.638
100 H211 H H54 N N N 0 9.198 -2.411 0.297
101 H221 H H55 N N N 0 8.458 -2.608 -1.31
102 H411 H H56 N N N 0 11.066 -0.896 0.627
103 H512 H H57 N N N 0 12.999 0.231 -0.402
104 H611 H H58 N N N 0 13.079 0.558 -2.841
105 H711 H H59 N N N 0 11.226 -0.243 -4.252
106 H811 H H60 N N N 0 9.297 -1.377 -3.224



0E9 : Chemical Bonds

Total Number of Bonds: 109
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 O1 C O doub 1.21 N N
2 C1 O2 C O sing 1.35 N N
3 O2 C2 O C sing 1.45 N N
4 C2 C3 C C sing 1.51 N N
5 C2 H21 C H sing 1.09 N N
6 C2 H22 C H sing 1.09 N N
7 C3 C4 C C doub 1.38 N Y
8 C3 C8 C C sing 1.38 N Y
9 C4 C5 C C sing 1.38 N Y
10 C4 H41 C H sing 1.08 N N
11 C5 C6 C C doub 1.38 N Y
12 C5 H51 C H sing 1.08 N N
13 C6 C7 C C sing 1.38 N Y
14 C6 H61 C H sing 1.08 N N
15 C7 C8 C C doub 1.38 N Y
16 C7 H71 C H sing 1.08 N N
17 C8 H81 C H sing 1.08 N N
18 N CA N C sing 1.47 N N
19 N H N H sing 0.97 N N
20 CA C C C sing 1.51 N N
21 CA CB C C sing 1.53 N N
22 CA HA C H sing 1.09 N N
23 C O C O doub 1.21 N N
24 CB CG1 C C sing 1.53 N N
25 CB CG2 C C sing 1.53 N N
26 CB HB C H sing 1.09 N N
27 CG1 HG11 C H sing 1.09 N N
28 CG1 HG12 C H sing 1.09 N N
29 CG1 HG13 C H sing 1.09 N N
30 CG2 HG21 C H sing 1.09 N N
31 CG2 HG22 C H sing 1.09 N N
32 CG2 HG23 C H sing 1.09 N N
33 C11 C21 C C sing 1.53 N N
34 C11 C1A C C sing 1.51 N N
35 C11 H11 C H sing 1.09 N N
36 C11 H12 C H sing 1.09 N N
37 C21 N2 C N sing 1.47 N N
38 C21 C31 C C sing 1.53 N N
39 C21 H2 C H sing 1.09 N N
40 N2 HN22 N H sing 0.97 N N
41 C31 O3 C O sing 1.43 N N
42 C31 C41 C C sing 1.53 N N
43 C31 H3 C H sing 1.09 N N
44 O3 HO3 O H sing 0.97 N N
45 C41 N4 C N sing 1.46 N N
46 C41 C51 C C sing 1.53 N N
47 C41 H4 C H sing 1.09 N N
48 N4 HN42 N H sing 0.97 N N
49 C51 C1B C C sing 1.51 N N
50 C51 H511 C H sing 1.09 N N
51 C51 H52 C H sing 1.09 N N
52 C1A C2A C C doub 1.38 N Y
53 C1A C6A C C sing 1.38 N Y
54 C2A C3A C C sing 1.38 N Y
55 C2A H2A C H sing 1.08 N N
56 C3A C4A C C doub 1.38 N Y
57 C3A H3A C H sing 1.08 N N
58 C4A C5A C C sing 1.38 N Y
59 C4A H4A C H sing 1.08 N N
60 C5A C6A C C doub 1.38 N Y
61 C5A H5A C H sing 1.08 N N
62 C6A H6A C H sing 1.08 N N
63 C1B C2B C C doub 1.38 N Y
64 C1B C6B C C sing 1.38 N Y
65 C2B C3B C C sing 1.38 N Y
66 C2B H2B C H sing 1.08 N N
67 C3B C4B C C doub 1.38 N Y
68 C3B H3B C H sing 1.08 N N
69 C4B C5B C C sing 1.38 N Y
70 C4B H4B C H sing 1.08 N N
71 C5B C6B C C doub 1.38 N Y
72 C5B H5B C H sing 1.08 N N
73 C6B H6B C H sing 1.08 N N
74 N1 CA1 N C sing 1.46 N N
75 N1 H1 N H sing 0.97 N N
76 CA1 C9 C C sing 1.51 N N
77 CA1 CB1 C C sing 1.53 N N
78 CA1 HA1 C H sing 1.09 N N
79 C9 O4 C O doub 1.21 N N
80 CB1 CG11 C C sing 1.53 N N
81 CB1 CG21 C C sing 1.53 N N
82 CB1 HB1 C H sing 1.09 N N
83 CG11 HG14 C H sing 1.09 N N
84 CG11 HG15 C H sing 1.09 N N
85 CG11 HG16 C H sing 1.09 N N
86 CG21 HG24 C H sing 1.09 N N
87 CG21 HG25 C H sing 1.09 N N
88 CG21 HG26 C H sing 1.09 N N
89 C12 O11 C O doub 1.21 N N
90 C12 O21 C O sing 1.35 N N
91 O21 C22 O C sing 1.45 N N
92 C22 C32 C C sing 1.51 N N
93 C22 H211 C H sing 1.09 N N
94 C22 H221 C H sing 1.09 N N
95 C32 C42 C C doub 1.38 N Y
96 C32 C81 C C sing 1.38 N Y
97 C42 C52 C C sing 1.38 N Y
98 C42 H411 C H sing 1.08 N N
99 C52 C61 C C doub 1.38 N Y
100 C52 H512 C H sing 1.08 N N
101 C61 C71 C C sing 1.38 N Y
102 C61 H611 C H sing 1.08 N N
103 C71 C81 C C doub 1.38 N Y
104 C71 H711 C H sing 1.08 N N
105 C81 H811 C H sing 1.08 N N
106 C1 N C N sing 1.35 N N
107 C N2 C N sing 1.35 N N
108 N4 C9 N C sing 1.35 N N
109 N1 C12 N C sing 1.35 N N



0E9 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0E9 9hvp Open in New Window Bound ligand 1 1