Chemical Components in the PDB

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P8U : Summary

Code

P8U

One-letter code

X

Molecule name

[(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 [(1~{S},2~{R})-2-cyclohexylcyclopropyl]methyl ~{N}-[(2~{S})-1-[[(1~{S},2~{S})-1-[bis(oxidanyl)-oxidanylidene-$l^{5}-sulfanyl]-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]amino]-4-methyl-1-oxidanylidene-pentan-2-yl]carbamate

Formula

C24 H42 N3 O8 S

Formal charge

1

Molecular weight

532.671 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC(C)C[CH](NC(=O)OC[CH]1C[CH]1C2CCCCC2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S+](O)(O)=O
SMILES OpenEye OEToolkits 2.0.7 CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)[S+](=O)(O)O)NC(=O)OCC2CC2C3CCCCC3
Canonical SMILES CACTVS 3.385 CC(C)C[C@H](NC(=O)OC[C@H]1C[C@@H]1C2CCCCC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)[S+](O)(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@@H](O)[S+](=O)(O)O)NC(=O)OC[C@H]2C[C@@H]2C3CCCCC3

IUPAC InChI

InChI=1S/C24H40N3O8S/c1-14(2)10-19(27-24(31)35-13-17-11-18(17)15-6-4-3-5-7-15)22(29)26-20(23(30)36(32,33)34)12-16-8-9-25-21(16)28/h14-20,23,30H,3-13H2,1-2H3,(H3-2,25,26,27,28,29,31,32,33,34)/q-1/p+2/t16-,17+,18+,19-,20-,23-/m0/s1

IUPAC InChI key

BNNIGFVXMNVYNU-MWOXCZGJSA-P
P8U

wwPDB Information

Atom count

78 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-05-26

Last modified at

2022-06-17

Status

Released

Obsoleted

Not Assigned



P8U : Atoms of Molecule

Total Number of Atoms: 78
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 1.109 -0.873 -0.02
2 C2 C C1 S N N 0 -0.13 -0.955 -0.798
3 C3 C C2 N N N 0 -0.363 -2.403 -1.235
4 C4 C C3 N N N 0 -1.555 -2.461 -2.192
5 C6 C C4 N N N 0 -1.204 -1.732 -3.49
6 C8 C C5 S N N 0 -3.651 0.018 0.342
7 C9 C C6 N N N 0 -4.673 0.792 -0.493
8 C10 C C7 S N N 0 -4.037 2.085 -1.007
9 C11 C C8 N N N 0 -5.028 2.869 -1.839
10 C16 C C9 S N N 0 5.865 -0.785 0.285
11 C17 C C10 R N N 0 7.266 -0.589 -0.298
12 C19 C C11 N N N 0 8.29 0.157 0.56
13 C20 C C12 N N N 0 7.775 1.567 0.857
14 C21 C C13 N N N 0 8.799 2.314 1.714
15 C22 C C14 N N N 0 10.127 2.404 0.96
16 C1 C C15 N N N 0 2.297 -0.798 -0.651
17 C12 C C16 N N N 0 -4.007 4.415 -0.438
18 C13 C C17 N N N 0 -3.701 3.029 0.172
19 C14 C C18 S N N 0 -4.302 -1.252 0.895
20 C15 C C19 N N N 0 4.683 -0.739 -0.686
21 C18 C C20 N N N 0 6.822 -1.974 0.178
22 C23 C C21 N N N 0 10.642 0.994 0.663
23 C24 C C22 N N N 0 9.618 0.248 -0.195
24 C5 C C23 N N N 0 -1.89 -3.921 -2.502
25 C7 C C24 N N N 0 -1.287 -0.494 0.05
26 N2 N N2 N N N 0 -2.508 -0.346 -0.5
27 N3 N N3 N N N 0 -4.994 4.168 -1.495
28 O1 O O1 N N N 0 2.338 -0.705 -1.862
29 O2 O O2 N N N 0 -5.748 2.395 -2.691
30 O3 O O3 N N N 0 -3.315 -2.041 1.562
31 O4 O O4 N N N 0 -1.119 -0.256 1.227
32 O5 O O5 N N N 0 3.44 -0.825 0.06
33 S1 S S1 N N Y 1 -5.609 -0.8 2.068
34 H1 H H1 N N N 0 1.074 -0.87 0.949
35 H2 H H2 N N N 0 -0.048 -0.318 -1.679
36 H3 H H3 N N N 0 0.527 -2.777 -1.741
37 H4 H H4 N N N 0 -0.569 -3.018 -0.359
38 H5 H H5 N N N 0 -2.417 -1.981 -1.728
39 H6 H H6 N N N 0 -0.391 -2.256 -3.993
40 H7 H H7 N N N 0 -2.077 -1.707 -4.141
41 H8 H H8 N N N 0 -0.892 -0.712 -3.262
42 H9 H H9 N N N 0 -3.31 0.641 1.168
43 H10 H H10 N N N 0 -4.989 0.182 -1.339
44 H11 H H11 N N N 0 -5.538 1.033 0.124
45 H12 H H12 N N N 0 -3.14 1.864 -1.586
46 H13 H H13 N N N 0 5.672 -0.381 1.279
47 H14 H H14 N N N 0 7.346 -0.428 -1.373
48 H15 H H15 N N N 0 8.44 -0.379 1.496
49 H16 H H16 N N N 0 7.625 2.104 -0.08
50 H17 H H17 N N N 0 6.829 1.503 1.394
51 H18 H H18 N N N 0 8.432 3.318 1.926
52 H19 H H19 N N N 0 8.949 1.777 2.651
53 H20 H H20 N N N 0 9.977 2.941 0.023
54 H21 H H21 N N N 0 10.856 2.936 1.571
55 H22 H H22 N N N 0 -4.425 5.076 0.321
56 H23 H H23 N N N 0 -3.101 4.85 -0.859
57 H24 H H24 N N N 0 -4.345 2.828 1.028
58 H25 H H25 N N N 0 -2.65 2.948 0.449
59 H26 H H26 N N N 0 -4.733 -1.826 0.074
60 H27 H H27 N N N 0 4.708 0.197 -1.244
61 H28 H H28 N N N 0 4.75 -1.578 -1.379
62 H29 H H29 N N N 0 7.259 -2.353 1.102
63 H30 H H30 N N N 0 6.609 -2.724 -0.584
64 H31 H H31 N N N 0 11.588 1.059 0.125
65 H32 H H32 N N N 0 10.792 0.458 1.599
66 H33 H H33 N N N 0 9.984 -0.757 -0.406
67 H34 H H34 N N N 0 9.468 0.785 -1.131
68 H35 H H35 N N N 0 -2.141 -4.44 -1.577
69 H36 H H36 N N N 0 -2.74 -3.963 -3.183
70 H37 H H37 N N N 0 -1.028 -4.401 -2.966
71 H38 H H38 N N N 0 -2.631 -0.481 -1.452
72 H39 H H39 N N N 0 -5.55 4.855 -1.896
73 H40 H H40 N N N 0 -2.584 -2.319 0.994
74 O6 O O6 N N Y 0 -6.138 -1.887 2.814
75 O7 O O7 N N Y 0 -5.043 0.221 3.045
76 O8 O O8 N N Y 0 -6.747 -0.154 1.291
77 H41 H H41 N N Y 0 -4.66 1.001 2.621
78 H42 H H42 N N Y 0 -7.494 0.121 1.841



P8U : Chemical Bonds

Total Number of Bonds: 80
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 C11 O C doub 1.21 N N
2 C18 C16 C C sing 1.53 N N
3 C18 C17 C C sing 1.53 N N
4 C16 C17 C C sing 1.53 N N
5 C16 C15 C C sing 1.53 N N
6 C11 N3 C N sing 1.34 N N
7 C11 C10 C C sing 1.51 N N
8 N3 C12 N C sing 1.47 N N
9 C17 C19 C C sing 1.53 N N
10 C15 O5 C O sing 1.45 N N
11 C19 C24 C C sing 1.53 N N
12 C19 C20 C C sing 1.53 N N
13 C24 C23 C C sing 1.53 N N
14 O1 C1 O C doub 1.22 N N
15 C23 C22 C C sing 1.53 N N
16 O5 C1 O C sing 1.35 N N
17 C10 C9 C C sing 1.53 N N
18 C10 C13 C C sing 1.55 N N
19 C1 N1 C N sing 1.35 N N
20 C12 C13 C C sing 1.54 N N
21 C20 C21 C C sing 1.53 N N
22 C9 C8 C C sing 1.53 N N
23 C21 C22 C C sing 1.53 N N
24 C6 C4 C C sing 1.53 N N
25 N1 C2 N C sing 1.47 N N
26 S1 C14 S C sing 1.81 N N
27 C2 C7 C C sing 1.51 N N
28 C2 C3 C C sing 1.53 N N
29 N2 C8 N C sing 1.47 N N
30 N2 C7 N C sing 1.35 N N
31 C8 C14 C C sing 1.53 N N
32 C7 O4 C O doub 1.21 N N
33 C4 C3 C C sing 1.53 N N
34 C4 C5 C C sing 1.53 N N
35 C14 O3 C O sing 1.43 N N
36 N1 H1 N H sing 0.97 N N
37 C2 H2 C H sing 1.09 N N
38 C3 H3 C H sing 1.09 N N
39 C3 H4 C H sing 1.09 N N
40 C4 H5 C H sing 1.09 N N
41 C6 H6 C H sing 1.09 N N
42 C6 H7 C H sing 1.09 N N
43 C6 H8 C H sing 1.09 N N
44 C8 H9 C H sing 1.09 N N
45 C9 H10 C H sing 1.09 N N
46 C9 H11 C H sing 1.09 N N
47 C10 H12 C H sing 1.09 N N
48 C16 H13 C H sing 1.09 N N
49 C17 H14 C H sing 1.09 N N
50 C19 H15 C H sing 1.09 N N
51 C20 H16 C H sing 1.09 N N
52 C20 H17 C H sing 1.09 N N
53 C21 H18 C H sing 1.09 N N
54 C21 H19 C H sing 1.09 N N
55 C22 H20 C H sing 1.09 N N
56 C22 H21 C H sing 1.09 N N
57 C12 H22 C H sing 1.09 N N
58 C12 H23 C H sing 1.09 N N
59 C13 H24 C H sing 1.09 N N
60 C13 H25 C H sing 1.09 N N
61 C14 H26 C H sing 1.09 N N
62 C15 H27 C H sing 1.09 N N
63 C15 H28 C H sing 1.09 N N
64 C18 H29 C H sing 1.09 N N
65 C18 H30 C H sing 1.09 N N
66 C23 H31 C H sing 1.09 N N
67 C23 H32 C H sing 1.09 N N
68 C24 H33 C H sing 1.09 N N
69 C24 H34 C H sing 1.09 N N
70 C5 H35 C H sing 1.09 N N
71 C5 H36 C H sing 1.09 N N
72 C5 H37 C H sing 1.09 N N
73 N2 H38 N H sing 0.97 N N
74 N3 H39 N H sing 0.97 N N
75 O3 H40 O H sing 0.97 N N
76 S1 O6 S O doub 1.42 N N
77 S1 O7 S O sing 1.52 N N
78 S1 O8 S O sing 1.52 N N
79 O7 H41 O H sing 0.97 N N
80 O8 H42 O H sing 0.97 N N



P8U : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
P8U 8czw Open in New Window Bound ligand 2 1