Chemical Components in the PDB

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U5G : Summary

Code

U5G

One-letter code

X

Molecule name

boceprevir (bound form)

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2S,5S)-N-[(2S,3R)-4-amino-1-cyclobutyl-3-hydroxy-4-oxobutan-2-yl]-3-[N-(tert-butylcarbamoyl)-3-methyl-L-valyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide
OpenEye OEToolkits 2.0.7 (1~{R},2~{S},5~{S})-~{N}-[(2~{S},3~{R})-4-azanyl-1-cyclobutyl-3-oxidanyl-4-oxidanylidene-butan-2-yl]-3-[(2~{S})-2-(~{tert}-butylcarbamoylamino)-3,3-dimethyl-butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide

Formula

C27 H47 N5 O5

Formal charge

0

Molecular weight

521.693 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(=O)(NC(C)(C)C)NC(C(C)(C)C)C(N1CC3C(C1C(=O)NC(CC2CCC2)C(O)C(=O)N)C3(C)C)=O
SMILES CACTVS 3.385 CC(C)(C)NC(=O)N[CH](C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](CC3CCC3)[CH](O)C(N)=O)C2(C)C)C(C)(C)C
SMILES OpenEye OEToolkits 2.0.7 CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)NC(C)(C)C)C(=O)NC(CC3CCC3)C(C(=O)N)O)C
Canonical SMILES CACTVS 3.385 CC(C)(C)NC(=O)N[C@H](C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](CC3CCC3)[C@@H](O)C(N)=O)C2(C)C)C(C)(C)C
Canonical SMILES OpenEye OEToolkits 2.0.7 CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)NC(C)(C)C)C(=O)N[C@@H](CC3CCC3)[C@H](C(=O)N)O)C

IUPAC InChI

InChI=1S/C27H47N5O5/c1-25(2,3)20(30-24(37)31-26(4,5)6)23(36)32-13-15-17(27(15,7)8)18(32)22(35)29-16(19(33)21(28)34)12-14-10-9-11-14/h14-20,33H,9-13H2,1-8H3,(H2,28,34)(H,29,35)(H2,30,31,37)/t15-,16-,17-,18-,19+,20+/m0/s1

IUPAC InChI key

FEBWCINGHXXUCV-GFLQDLJJSA-N

Has sub-components

TBB , TBG , 12L , 12N
U5G

wwPDB Information

Atom count

84 (37 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAD

Is modified

No

Standard parent

Not Assigned

Defined at

2020-04-23

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



U5G : Atoms of Molecule

Total Number of Atoms: 84
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C28 C C1 N N N 0 4.735 0.417 -0.029
2 N29 N N1 N N N 0 5.749 1.038 -0.663
3 O34 O O1 N N N 0 4.968 -0.489 0.748
4 C30 C C2 N N N 0 7.132 0.623 -0.414
5 C31 C C3 N N N 0 8.081 1.483 -1.252
6 C32 C C4 N N N 0 7.459 0.8 1.07
7 C33 C C5 N N N 0 7.3 -0.848 -0.802
8 N27 N N2 N N N 0 3.463 0.802 -0.253
9 C22 C C6 S N N 0 2.361 0.131 0.44
10 C23 C C7 N N N 0 2.158 0.77 1.815
11 C24 C C8 N N N 0 1.76 2.237 1.641
12 C25 C C9 N N N 0 1.051 0.026 2.565
13 C26 C C10 N N N 0 3.46 0.686 2.614
14 C21 C C11 N N N 0 1.098 0.271 -0.371
15 O35 O O2 N N N 0 0.951 1.226 -1.103
16 N20 N N3 N N N 0 0.133 -0.666 -0.281
17 C19 C C12 N N N 0 0.164 -1.933 0.486
18 C13 C C13 S N N 0 -1.202 -0.658 -0.923
19 C14 C C14 R N N 0 -1.429 -2.119 -1.367
20 C15 C C15 S N N 0 -0.525 -2.963 -0.435
21 C16 C C16 N N N 0 -0.24 -2.891 -1.943
22 C17 C C17 N N N 0 0.977 -2.08 -2.39
23 C18 C C18 N N N 0 -0.545 -4.136 -2.778
24 C12 C C19 N N N 0 -2.259 -0.24 0.067
25 O36 O O3 N N N 0 -2.03 -0.293 1.257
26 N11 N N4 N N N 0 -3.458 0.194 -0.37
27 C05 C C20 S N N 0 -4.485 0.601 0.592
28 C06 C C21 N N N 0 -5.444 1.589 -0.073
29 C07 C C22 N N N 0 -4.689 2.873 -0.427
30 C10 C C23 N N N 0 -5.592 3.982 -0.992
31 C03 C C26 R N N 0 -5.264 -0.631 1.058
32 C08 C C24 N N N 0 -4.012 2.829 -1.807
33 C09 C C25 N N N 0 -4.458 4.29 -1.985
34 O04 O O4 N N Y 0 -5.886 -1.255 -0.068
35 O01 O O5 N N N 0 -4.122 -2.691 1.21
36 C02 C C27 N N N 0 -4.319 -1.605 1.713
37 N37 N N5 N N N 0 -3.693 -1.269 2.859
38 H1 H H1 N N N 0 5.564 1.761 -1.283
39 H2 H H2 N N N 0 7.961 2.53 -0.976
40 H3 H H3 N N N 0 9.11 1.174 -1.067
41 H4 H H4 N N N 0 7.848 1.357 -2.309
42 H5 H H5 N N N 0 6.783 0.187 1.666
43 H6 H H6 N N N 0 8.488 0.491 1.254
44 H7 H H7 N N N 0 7.339 1.847 1.346
45 H8 H H8 N N N 0 7.067 -0.973 -1.86
46 H9 H H9 N N N 0 8.329 -1.156 -0.618
47 H10 H H10 N N N 0 6.624 -1.46 -0.206
48 H11 H H11 N N N 0 3.278 1.525 -0.873
49 H12 H H12 N N N 0 2.599 -0.926 0.562
50 H13 H H13 N N N 0 0.832 2.297 1.072
51 H14 H H14 N N N 0 1.615 2.693 2.621
52 H18 H H18 N N N 0 0.109 0.14 2.029
53 H15 H H15 N N N 0 2.548 2.767 1.107
54 H16 H H16 N N N 0 1.305 -1.032 2.632
55 H17 H H17 N N N 0 0.951 0.44 3.568
56 H19 H H19 N N N 0 4.249 1.216 2.079
57 H20 H H20 N N N 0 3.316 1.142 3.593
58 H21 H H21 N N N 0 3.744 -0.359 2.737
59 H22 H H22 N N N 0 1.193 -2.231 0.686
60 H23 H H23 N N N 0 -0.39 -1.826 1.418
61 H24 H H24 N N N 0 -1.205 0.006 -1.787
62 H25 H H25 N N N 0 -2.443 -2.413 -1.639
63 H26 H H26 N N N 0 -0.874 -3.891 0.017
64 H27 H H27 N N N 0 1.377 -1.526 -1.541
65 H28 H H28 N N N 0 1.742 -2.754 -2.776
66 H29 H H29 N N N 0 0.681 -1.381 -3.172
67 H30 H H30 N N N 0 -1.152 -3.856 -3.639
68 H31 H H31 N N N 0 0.388 -4.582 -3.121
69 H32 H H32 N N N 0 -1.09 -4.858 -2.169
70 H33 H H33 N N N 0 -3.641 0.236 -1.322
71 H34 H H34 N N N 0 -4.01 1.076 1.45
72 H35 H H35 N N N 0 -5.851 1.145 -0.982
73 H36 H H36 N N N 0 -6.258 1.824 0.613
74 H37 H H37 N N N 0 -4.031 3.211 0.373
75 H38 H H38 N N N 0 -6.499 3.608 -1.467
76 H39 H H39 N N N 0 -5.786 4.789 -0.286
77 H40 H H40 N N N 0 -2.93 2.705 -1.759
78 H41 H H41 N N N 0 -4.487 2.139 -2.505
79 H42 H H42 N N N 0 -4.81 4.52 -2.991
80 H43 H H43 N N N 0 -3.736 5.016 -1.612
81 H44 H H44 N N Y 0 -5.264 -1.55 -0.747
82 H45 H H45 N N N 0 -6.028 -0.328 1.774
83 H46 H H46 N N N 0 -3.085 -1.896 3.28
84 H47 H H47 N N N 0 -3.85 -0.401 3.261



U5G : Chemical Bonds

Total Number of Bonds: 86
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O01 C02 O C doub 1.21 N N
2 C06 C07 C C sing 1.53 N N
3 C06 C05 C C sing 1.53 N N
4 C08 C07 C C sing 1.54 N N
5 C08 C09 C C sing 1.54 N N
6 C02 C03 C C sing 1.51 N N
7 C02 N37 C N sing 1.35 N N
8 C03 C05 C C sing 1.53 N N
9 C03 O04 C O sing 1.43 N N
10 C07 C10 C C sing 1.54 N N
11 C05 N11 C N sing 1.46 N N
12 N11 C12 N C sing 1.35 N N
13 O35 C21 O C doub 1.21 N N
14 C09 C10 C C sing 1.54 N N
15 C32 C30 C C sing 1.53 N N
16 C12 C13 C C sing 1.51 N N
17 C12 O36 C O doub 1.21 N N
18 C13 N20 C N sing 1.48 N N
19 C13 C14 C C sing 1.54 N N
20 C25 C23 C C sing 1.53 N N
21 C21 N20 C N sing 1.35 N N
22 C21 C22 C C sing 1.51 N N
23 N29 C30 N C sing 1.47 N N
24 N29 C28 N C sing 1.35 N N
25 N27 C28 N C sing 1.35 N N
26 N27 C22 N C sing 1.46 N N
27 C31 C30 C C sing 1.53 N N
28 C17 C16 C C sing 1.53 N N
29 C30 C33 C C sing 1.53 N N
30 N20 C19 N C sing 1.48 N N
31 C14 C16 C C sing 1.53 N N
32 C14 C15 C C sing 1.55 N N
33 C28 O34 C O doub 1.22 N N
34 C22 C23 C C sing 1.53 N N
35 C16 C18 C C sing 1.53 N N
36 C16 C15 C C sing 1.54 N N
37 C23 C24 C C sing 1.53 N N
38 C23 C26 C C sing 1.53 N N
39 C19 C15 C C sing 1.54 N N
40 N29 H1 N H sing 0.97 N N
41 C31 H2 C H sing 1.09 N N
42 C31 H3 C H sing 1.09 N N
43 C31 H4 C H sing 1.09 N N
44 C32 H5 C H sing 1.09 N N
45 C32 H6 C H sing 1.09 N N
46 C32 H7 C H sing 1.09 N N
47 C33 H8 C H sing 1.09 N N
48 C33 H9 C H sing 1.09 N N
49 C33 H10 C H sing 1.09 N N
50 N27 H11 N H sing 0.97 N N
51 C22 H12 C H sing 1.09 N N
52 C24 H13 C H sing 1.09 N N
53 C24 H14 C H sing 1.09 N N
54 C24 H15 C H sing 1.09 N N
55 C25 H16 C H sing 1.09 N N
56 C25 H17 C H sing 1.09 N N
57 C25 H18 C H sing 1.09 N N
58 C26 H19 C H sing 1.09 N N
59 C26 H20 C H sing 1.09 N N
60 C26 H21 C H sing 1.09 N N
61 C19 H22 C H sing 1.09 N N
62 C19 H23 C H sing 1.09 N N
63 C13 H24 C H sing 1.09 N N
64 C14 H25 C H sing 1.09 N N
65 C15 H26 C H sing 1.09 N N
66 C17 H27 C H sing 1.09 N N
67 C17 H28 C H sing 1.09 N N
68 C17 H29 C H sing 1.09 N N
69 C18 H30 C H sing 1.09 N N
70 C18 H31 C H sing 1.09 N N
71 C18 H32 C H sing 1.09 N N
72 N11 H33 N H sing 0.97 N N
73 C05 H34 C H sing 1.09 N N
74 C06 H35 C H sing 1.09 N N
75 C06 H36 C H sing 1.09 N N
76 C07 H37 C H sing 1.09 N N
77 C10 H38 C H sing 1.09 N N
78 C10 H39 C H sing 1.09 N N
79 C08 H40 C H sing 1.09 N N
80 C08 H41 C H sing 1.09 N N
81 C09 H42 C H sing 1.09 N N
82 C09 H43 C H sing 1.09 N N
83 O04 H44 O H sing 0.97 N N
84 C03 H45 C H sing 1.09 N N
85 N37 H46 N H sing 0.97 N N
86 N37 H47 N H sing 0.97 N N



U5G : Used in PDB Entries

Total Number of PDB Entries: 9
Ligand Code PDB Entry ID Type Total Distinct
U5G 2oc8 Open in New Window Bound ligand 1 1
U5G 6wnp Open in New Window Bound ligand 1 1
U5G 6xqu Open in New Window Bound ligand 1 1
U5G 6zru Open in New Window Bound ligand 1 1
U5G 7brp Open in New Window Bound ligand 2 1
U5G 7c6s Open in New Window Bound ligand 1 1
U5G 7com Open in New Window Bound ligand 2 1
U5G 7k40 Open in New Window Bound ligand 1 1
U5G 7nbr Open in New Window Bound ligand 1 1