Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

PB0 : Summary

Code

PB0

One-letter code

X

Molecule name

(2S)-2-[(3R)-3-(acetylamino)-3-(2-methylpropyl)-2-oxopyrrolidin-1-yl]-N-{(1R,2S)-3-(3,5-difluorophenyl)-1-hydroxy-1-[(2R,4R)-4-propoxypyrrolidin-2-yl]propan-2-yl}-4-phenylbutanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (2S)-2-[(3R)-3-(acetylamino)-3-(2-methylpropyl)-2-oxopyrrolidin-1-yl]-N-{(1R,2S)-3-(3,5-difluorophenyl)-1-hydroxy-1-[(2R,4R)-4-propoxypyrrolidin-2-yl]propan-2-yl}-4-phenylbutanamide
OpenEye OEToolkits 1.7.0 (2S)-2-[(3R)-3-acetamido-3-(2-methylpropyl)-2-oxo-pyrrolidin-1-yl]-N-[(1R,2S)-3-(3,5-difluorophenyl)-1-hydroxy-1-[(2R,4R)-4-propoxypyrrolidin-2-yl]propan-2-yl]-4-phenyl-butanamide

Formula

C36 H50 F2 N4 O5

Formal charge

0

Molecular weight

656.803 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Fc1cc(cc(F)c1)CC(NC(=O)C(N2C(=O)C(NC(=O)C)(CC2)CC(C)C)CCc3ccccc3)C(O)C4NCC(OCCC)C4
SMILES CACTVS 3.370 CCCO[CH]1CN[CH](C1)[CH](O)[CH](Cc2cc(F)cc(F)c2)NC(=O)[CH](CCc3ccccc3)N4CC[C](CC(C)C)(NC(C)=O)C4=O
SMILES OpenEye OEToolkits 1.7.0 CCCOC1CC(NC1)C(C(Cc2cc(cc(c2)F)F)NC(=O)C(CCc3ccccc3)N4CCC(C4=O)(CC(C)C)NC(=O)C)O
Canonical SMILES CACTVS 3.370 CCCO[C@H]1CN[C@H](C1)[C@@H](O)[C@H](Cc2cc(F)cc(F)c2)NC(=O)[C@H](CCc3ccccc3)N4CC[C@@](CC(C)C)(NC(C)=O)C4=O
Canonical SMILES OpenEye OEToolkits 1.7.0 CCCO[C@@H]1C[C@@H](NC1)[C@H]([C@H](Cc2cc(cc(c2)F)F)NC(=O)[C@H](CCc3ccccc3)N4CC[C@@](C4=O)(CC(C)C)NC(=O)C)O

IUPAC InChI

InChI=1S/C36H50F2N4O5/c1-5-15-47-29-20-30(39-22-29)33(44)31(18-26-16-27(37)19-28(38)17-26)40-34(45)32(12-11-25-9-7-6-8-10-25)42-14-13-36(35(42)46,21-23(2)3)41-24(4)43/h6-10,16-17,19,23,29-33,39,44H,5,11-15,18,20-22H2,1-4H3,(H,40,45)(H,41,43)/t29-,30-,31+,32+,33-,36+/m1/s1

IUPAC InChI key

LPZOLMFQGUDKQH-ZXWXCOCLSA-N
PB0

wwPDB Information

Atom count

97 (47 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2011-03-21

Last modified at

2011-08-26

Status

Released

Obsoleted

Not Assigned



PB0 : Atoms of Molecule

Total Number of Atoms: 97
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 -1.721 7.029 -1.011
2 C2 C C2 N Y N 0 -1.272 6.448 -2.182
3 C3 C C3 N Y N 0 -2.394 6.268 -0.075
4 C4 C C4 N Y N 0 -1.497 5.104 -2.417
5 C5 C C5 N Y N 0 -2.619 4.924 -0.309
6 C6 C C6 N Y N 0 0.178 -2.847 -2.683
7 C7 C C7 N Y N 0 1.247 -3.827 -0.778
8 C8 C C8 N Y N 0 -0.868 -4.671 -1.53
9 C9 C C9 N Y N 0 -2.17 4.342 -1.48
10 C10 C C10 N Y N 0 1.236 -2.891 -1.795
11 C11 C C11 N Y N 0 -0.875 -3.737 -2.552
12 C12 C C12 N Y N 0 0.198 -4.722 -0.649
13 C13 C C13 N N N 0 -2.805 0.271 0.647
14 C14 C C14 N N N 0 -3.253 -1.727 2.84
15 C15 C C15 N N N 0 -0.292 -0.222 -1.012
16 C16 C C16 N N N 0 -4.96 -0.391 -0.214
17 C17 C C17 N N N 0 5.749 0.542 -0.579
18 C18 C C18 N N N 0 -3.846 -0.513 -1.275
19 C19 C C19 N N N 0 5.657 -0.7 1.532
20 C20 C C20 R N N 0 6.627 0.037 0.589
21 C21 C C21 R N N 0 4.518 -0.396 -0.518
22 C22 C C22 R N N 0 -4.142 -0.279 1.093
23 C23 C C23 N N N 0 -2.985 -3.095 3.411
24 C24 C C24 N N N 0 10.412 1.754 3.173
25 C25 C C25 N N N 0 -6.657 0.92 3.745
26 C26 C C26 N N N 0 -7.116 -0.133 1.526
27 C27 C C27 N N N 0 -2.416 2.878 -1.736
28 C28 C C28 N N N 0 2.378 -1.919 -1.936
29 C29 C C29 N N N 0 -4.819 0.687 2.068
30 C30 C C30 N N N 0 9.056 2.081 2.545
31 C31 C C31 N N N 0 -1.247 2.06 -1.184
32 C32 C C32 N N N 0 8.501 0.835 1.852
33 C33 C C33 S N N 0 -1.497 0.573 -1.444
34 C34 C C34 R N N 0 3.299 0.27 -1.159
35 C35 C C35 N N N 0 -6.08 0.034 2.639
36 C36 C C36 S N N 0 2.101 -0.679 -1.084
37 N37 N N37 N N N 0 4.306 -0.586 0.94
38 N38 N N38 N N N 0 -2.67 0.134 -0.683
39 N39 N N39 N N N 0 -3.974 -1.597 1.709
40 N40 N N40 N N N 0 0.906 0.003 -1.588
41 O41 O O41 N N N 0 -1.977 0.767 1.382
42 O42 O O42 N N N 0 -2.818 -0.741 3.398
43 O43 O O43 N N N 0 -0.4 -1.064 -0.146
44 O44 O O44 N N N 0 3.583 0.571 -2.526
45 O45 O O45 N N N 0 7.234 1.139 1.266
46 F46 F F46 N N N 0 -1.91 -3.693 -3.42
47 F47 F F47 N N N 0 0.215 -5.644 0.339
48 H1 H H1 N N N 0 -1.541 8.078 -0.826
49 H2 H H2 N N N 0 -0.746 7.043 -2.914
50 H3 H H3 N N N 0 -2.744 6.722 0.84
51 H4 H H4 N N N 0 -1.147 4.649 -3.332
52 H5 H H5 N N N 0 -3.145 4.329 0.423
53 H6 H H6 N N N 0 0.17 -2.115 -3.478
54 H7 H H7 N N N 0 2.074 -3.861 -0.085
55 H8 H H8 N N N 0 -1.686 -5.368 -1.429
56 H16 H H16 N N N 0 -5.559 0.505 -0.377
57 H16A H H16A N N N 0 -5.589 -1.282 -0.204
58 H17 H H17 N N N 0 5.452 1.579 -0.418
59 H17A H H17A N N N 0 6.271 0.433 -1.529
60 H18 H H18 N N N 0 -3.635 -1.562 -1.482
61 H18A H H18A N N N 0 -4.139 0.001 -2.19
62 H19 H H19 N N N 0 5.941 -1.749 1.61
63 H19A H H19A N N N 0 5.67 -0.237 2.518
64 H20 H H20 N N N 0 7.39 -0.648 0.22
65 H21 H H21 N N N 0 4.735 -1.347 -1.005
66 H23 H H23 N N N 0 -2.017 -3.452 3.061
67 H23A H H23A N N N 0 -2.98 -3.04 4.499
68 H23B H H23B N N N 0 -3.765 -3.784 3.086
69 H24 H H24 N N N 0 10.807 2.642 3.667
70 H24A H H24A N N N 0 10.291 0.955 3.904
71 H24B H H24B N N N 0 11.105 1.433 2.395
72 H25 H H25 N N N 0 -7.555 0.455 4.152
73 H25A H H25A N N N 0 -5.918 1.039 4.537
74 H25B H H25B N N N 0 -6.909 1.897 3.333
75 H26 H H26 N N N 0 -7.223 0.807 0.985
76 H26A H H26A N N N 0 -6.789 -0.913 0.839
77 H26B H H26B N N N 0 -8.076 -0.412 1.962
78 H27 H H27 N N N 0 -3.339 2.572 -1.242
79 H27A H H27A N N N 0 -2.506 2.706 -2.809
80 H28 H H28 N N N 0 3.301 -2.391 -1.6
81 H28A H H28A N N N 0 2.48 -1.626 -2.981
82 H29 H H29 N N N 0 -4.133 0.924 2.881
83 H29A H H29A N N N 0 -5.09 1.602 1.543
84 H31A H H31A N N N 0 -1.158 2.231 -0.112
85 H30 H H30 N N N 0 8.363 2.402 3.323
86 H30A H H30A N N N 0 9.177 2.88 1.814
87 H31 H H31 N N N 0 -0.325 2.365 -1.679
88 H32 H H32 N N N 0 9.194 0.513 1.074
89 H32A H H32A N N N 0 8.38 0.036 2.583
90 H33 H H33 N N N 0 -1.674 0.415 -2.508
91 H34 H H34 N N N 0 3.066 1.192 -0.625
92 H35 H H35 N N N 0 -5.828 -0.944 3.051
93 H36 H H36 N N N 0 1.938 -0.978 -0.049
94 HN37 H HN37 N N N 0 3.761 -1.415 1.121
95 HN39 H HN39 N N N 0 -4.383 -2.378 1.303
96 HN40 H HN40 N N N 0 0.976 0.615 -2.337
97 HO44 H HO44 N N N 0 3.8 -0.204 -3.063



PB0 : Chemical Bonds

Total Number of Bonds: 100
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C3 C C doub 1.38 N Y
2 C1 C2 C C sing 1.38 N Y
3 C1 H1 C H sing 1.08 N N
4 C2 C4 C C doub 1.38 N Y
5 C2 H2 C H sing 1.08 N N
6 C3 C5 C C sing 1.38 N Y
7 C3 H3 C H sing 1.08 N N
8 C4 C9 C C sing 1.38 N Y
9 C4 H4 C H sing 1.08 N N
10 C5 C9 C C doub 1.38 N Y
11 C5 H5 C H sing 1.08 N N
12 C11 C6 C C doub 1.38 N Y
13 C6 C10 C C sing 1.38 N Y
14 C6 H6 C H sing 1.08 N N
15 C12 C7 C C sing 1.38 N Y
16 C10 C7 C C doub 1.38 N Y
17 C7 H7 C H sing 1.08 N N
18 C11 C8 C C sing 1.38 N Y
19 C8 C12 C C doub 1.38 N Y
20 C8 H8 C H sing 1.08 N N
21 C9 C27 C C sing 1.51 N N
22 C10 C28 C C sing 1.51 N N
23 F46 C11 F C sing 1.35 N N
24 C12 F47 C F sing 1.35 N N
25 N38 C13 N C sing 1.34 N N
26 C13 O41 C O doub 1.21 N N
27 C13 C22 C C sing 1.51 N N
28 O42 C14 O C doub 1.21 N N
29 C23 C14 C C sing 1.51 N N
30 C14 N39 C N sing 1.35 N N
31 C33 C15 C C sing 1.51 N N
32 O43 C15 O C doub 1.21 N N
33 C15 N40 C N sing 1.35 N N
34 C16 C18 C C sing 1.54 N N
35 C16 C22 C C sing 1.55 N N
36 C16 H16 C H sing 1.09 N N
37 C16 H16A C H sing 1.09 N N
38 C17 C20 C C sing 1.55 N N
39 C17 C21 C C sing 1.55 N N
40 C17 H17 C H sing 1.09 N N
41 C17 H17A C H sing 1.09 N N
42 C18 N38 C N sing 1.47 N N
43 C18 H18 C H sing 1.09 N N
44 C18 H18A C H sing 1.09 N N
45 C20 C19 C C sing 1.54 N N
46 C19 N37 C N sing 1.48 N N
47 C19 H19 C H sing 1.09 N N
48 C19 H19A C H sing 1.09 N N
49 C20 O45 C O sing 1.43 N N
50 C20 H20 C H sing 1.09 N N
51 C21 C34 C C sing 1.53 N N
52 C21 N37 C N sing 1.49 N N
53 C21 H21 C H sing 1.09 N N
54 N39 C22 N C sing 1.46 N N
55 C22 C29 C C sing 1.53 N N
56 C23 H23 C H sing 1.09 N N
57 C23 H23A C H sing 1.09 N N
58 C23 H23B C H sing 1.09 N N
59 C30 C24 C C sing 1.53 N N
60 C24 H24 C H sing 1.09 N N
61 C24 H24A C H sing 1.09 N N
62 C24 H24B C H sing 1.09 N N
63 C35 C25 C C sing 1.53 N N
64 C25 H25 C H sing 1.09 N N
65 C25 H25A C H sing 1.09 N N
66 C25 H25B C H sing 1.09 N N
67 C26 C35 C C sing 1.53 N N
68 C26 H26 C H sing 1.09 N N
69 C26 H26A C H sing 1.09 N N
70 C26 H26B C H sing 1.09 N N
71 C27 C31 C C sing 1.53 N N
72 C27 H27 C H sing 1.09 N N
73 C27 H27A C H sing 1.09 N N
74 C36 C28 C C sing 1.53 N N
75 C28 H28 C H sing 1.09 N N
76 C28 H28A C H sing 1.09 N N
77 C29 C35 C C sing 1.53 N N
78 C29 H29 C H sing 1.09 N N
79 C29 H29A C H sing 1.09 N N
80 C32 C30 C C sing 1.53 N N
81 C30 H30 C H sing 1.09 N N
82 C30 H30A C H sing 1.09 N N
83 C31 C33 C C sing 1.53 N N
84 C31 H31 C H sing 1.09 N N
85 C31 H31A C H sing 1.09 N N
86 C32 O45 C O sing 1.43 N N
87 C32 H32 C H sing 1.09 N N
88 C32 H32A C H sing 1.09 N N
89 C33 N38 C N sing 1.47 N N
90 C33 H33 C H sing 1.09 N N
91 C36 C34 C C sing 1.53 N N
92 C34 O44 C O sing 1.43 N N
93 C34 H34 C H sing 1.09 N N
94 C35 H35 C H sing 1.09 N N
95 N40 C36 N C sing 1.47 N N
96 C36 H36 C H sing 1.09 N N
97 N37 HN37 N H sing 1.01 N N
98 N39 HN39 N H sing 0.97 N N
99 N40 HN40 N H sing 0.97 N N
100 O44 HO44 O H sing 0.97 N N



PB0 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
PB0 3r2f Open in New Window Bound ligand 4 1