Chemical Components in the PDB

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X6T : Summary

Code

X6T

One-letter code

X

Molecule name

(1R,2S,5S)-N-{(2S,3R)-4-(3,3-dimethylazetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (1R,2S,5S)-N-{(2S,3R)-4-(3,3-dimethylazetidin-1-yl)-3-hydroxy-4-oxo-1-[(3S)-2-oxopiperidin-3-yl]butan-2-yl}-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-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-(3,3-dimethylazetidin-1-yl)-3-oxidanyl-4-oxidanylidene-1-[(3~{S})-2-oxidanylidenepiperidin-3-yl]butan-2-yl]-3-[(2~{S})-3,3-dimethyl-2-[2,2,2-tris(fluoranyl)ethanoylamino]butanoyl]-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide

Formula

C30 H46 F3 N5 O6

Formal charge

0

Molecular weight

629.711 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 CC1(C)C2C(C(=O)NC(CC3CCCNC3=O)C(O)C(=O)N3CC(C)(C)C3)N(CC21)C(=O)C(NC(=O)C(F)(F)F)C(C)(C)C
SMILES CACTVS 3.385 CC(C)(C)[CH](NC(=O)C(F)(F)F)C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](C[CH]3CCCNC3=O)[CH](O)C(=O)N4CC(C)(C)C4)C2(C)C
SMILES OpenEye OEToolkits 2.0.7 CC1(CN(C1)C(=O)C(C(CC2CCCNC2=O)NC(=O)C3C4C(C4(C)C)CN3C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)O)C
Canonical SMILES CACTVS 3.385 CC(C)(C)[C@H](NC(=O)C(F)(F)F)C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCCNC3=O)[C@@H](O)C(=O)N4CC(C)(C)C4)C2(C)C
Canonical SMILES OpenEye OEToolkits 2.0.7 CC1(CN(C1)C(=O)[C@@H]([C@H](C[C@@H]2CCCNC2=O)NC(=O)[C@@H]3[C@@H]4[C@@H](C4(C)C)CN3C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)O)C

IUPAC InChI

InChI=1S/C30H46F3N5O6/c1-27(2,3)21(36-26(44)30(31,32)33)25(43)38-12-16-18(29(16,6)7)19(38)23(41)35-17(11-15-9-8-10-34-22(15)40)20(39)24(42)37-13-28(4,5)14-37/h15-21,39H,8-14H2,1-7H3,(H,34,40)(H,35,41)(H,36,44)/t15-,16-,17-,18-,19-,20+,21+/m0/s1

IUPAC InChI key

KOJLJTKYOSKMNV-YTNBPZCUSA-N
X6T

wwPDB Information

Atom count

90 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-11-02

Last modified at

2023-10-06

Status

Released

Obsoleted

Not Assigned



X6T : Atoms of Molecule

Total Number of Atoms: 90
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 -1.519 0.927 -0.274
2 N3 N N2 N N N 0 1.984 0.465 -1.381
3 C4 C C1 S N N 0 -0.834 3.114 0.42
4 C5 C C2 N N N 0 -1.419 3.66 -0.884
5 C6 C C3 N N N 0 -2.726 3.042 -1.384
6 C7 C C4 N N N 0 -1.249 5.155 -1.161
7 C8 C C5 N N N 0 -1.359 1.759 0.942
8 C10 C C6 S N N 0 -3.57 -0.236 0.473
9 C13 C C7 N N N 0 -1.872 -0.974 2.15
10 C15 C C8 N N N 0 -5.999 -0.42 0.419
11 C17 C C9 S N N 0 3.131 -0.338 -0.949
12 C20 C C10 N N N 0 4.933 3.112 1.146
13 C21 C C11 N N N 0 4.38 2.27 2.31
14 C22 C C12 N N N 0 2.861 2.359 2.469
15 C24 C C13 N N N 0 4.849 1.04 1.511
16 C26 C C14 S N N 0 4.129 -2.628 -0.946
17 C28 C C15 N N N 0 5.075 -4.926 -0.908
18 C1 C C16 N N N 0 0.88 0.532 -0.612
19 O1 O O1 N N N 0 0.868 0.002 0.479
20 C2 C C17 S N N 0 -0.341 1.264 -1.106
21 N2 N N3 N N N 0 -4.818 -0.602 -0.203
22 O2 O O2 N N N 0 -6.03 0.046 1.538
23 C3 C C18 R N N 0 -0.163 2.788 -0.93
24 O3 O O3 N N N 0 -2.544 -0.492 -1.637
25 N4 N N4 N N N 0 4.752 1.904 0.318
26 O4 O O4 N N N 0 4.533 2.613 -1.773
27 N5 N N5 N N N 0 4.196 -3.96 1.168
28 O5 O O5 N N N 0 4.358 0.284 -2.936
29 O6 O O6 N N N 0 3.672 -1.838 1.203
30 C9 C C19 N N N 0 -2.508 0.056 -0.555
31 C11 C C20 N N N 0 -3.114 -1.394 1.362
32 C12 C C21 N N N 0 -4.235 -1.762 2.336
33 C14 C C22 N N N 0 -2.778 -2.606 0.49
34 C16 C C23 N N N 0 -7.282 -0.796 -0.276
35 C18 C C24 R N N 0 4.419 0.27 -1.509
36 C19 C C25 N N N 0 4.572 1.68 -0.999
37 C23 C C26 N N N 0 5.132 2.471 3.628
38 C25 C C27 N N N 0 2.975 -1.769 -1.467
39 C27 C C28 N N N 0 4.096 -3.995 -1.634
40 C29 C C29 N N N 0 4.536 -5.205 0.495
41 C30 C C30 N N N 0 3.989 -2.802 0.539
42 F1 F F1 N N N 0 -7.266 -2.162 -0.579
43 F2 F F2 N N N 0 -8.366 -0.517 0.563
44 F3 F F3 N N N 0 -7.406 -0.058 -1.459
45 H1 H H1 N N N 0 2.02 0.949 -2.221
46 H2 H H2 N N N 0 -0.382 3.8 1.136
47 H3 H H3 N N N 0 -3.529 3.774 -1.304
48 H4 H H4 N N N 0 -2.61 2.742 -2.426
49 H5 H H5 N N N 0 -2.969 2.168 -0.78
50 H6 H H6 N N N 0 -0.58 5.589 -0.418
51 H7 H H7 N N N 0 -0.827 5.295 -2.156
52 H8 H H8 N N N 0 -2.22 5.647 -1.106
53 H9 H H9 N N N 0 -2.319 1.89 1.441
54 H10 H H10 N N N 0 -0.635 1.306 1.62
55 H11 H H11 N N N 0 -3.736 0.65 1.087
56 H12 H H12 N N N 0 -2.129 -0.158 2.826
57 H13 H H13 N N N 0 -1.503 -1.821 2.728
58 H14 H H14 N N N 0 -1.097 -0.642 1.458
59 H15 H H15 N N N 0 3.177 -0.348 0.14
60 H16 H H16 N N N 0 4.287 3.942 0.859
61 H17 H H17 N N N 0 5.974 3.408 1.274
62 H18 H H18 N N N 0 2.379 2.007 1.556
63 H19 H H19 N N N 0 2.546 1.74 3.308
64 H20 H H20 N N N 0 2.576 3.395 2.654
65 H21 H H21 N N N 0 5.866 0.726 1.744
66 H22 H H22 N N N 0 4.136 0.215 1.516
67 H23 H H23 N N N 0 5.076 -2.135 -1.165
68 H24 H H24 N N N 0 5.164 -5.863 -1.458
69 H25 H H25 N N N 0 6.052 -4.448 -0.839
70 H26 H H26 N N N 0 -0.532 1.02 -2.151
71 H27 H H27 N N N 0 -4.793 -0.974 -1.098
72 H28 H H28 N N N 0 0.789 3.232 -1.221
73 H29 H H29 N N N 0 4.115 -3.974 2.134
74 H30 H H30 N N N 0 3.621 0.799 -3.293
75 H31 H H31 N N N 0 -4.474 -0.9 2.958
76 H32 H H32 N N N 0 -5.12 -2.062 1.775
77 H33 H H33 N N N 0 -3.91 -2.588 2.97
78 H34 H H34 N N N 0 -2.453 -3.431 1.123
79 H35 H H35 N N N 0 -3.663 -2.905 -0.072
80 H36 H H36 N N N 0 -1.979 -2.343 -0.204
81 H37 H H37 N N N 0 5.272 -0.327 -1.187
82 H38 H H38 N N N 0 5.069 3.517 3.926
83 H39 H H39 N N N 0 4.686 1.845 4.4
84 H40 H H40 N N N 0 6.178 2.194 3.495
85 H41 H H41 N N N 0 2.028 -2.181 -1.118
86 H42 H H42 N N N 0 2.989 -1.764 -2.557
87 H43 H H43 N N N 0 3.089 -4.408 -1.581
88 H44 H H44 N N N 0 4.395 -3.888 -2.676
89 H45 H H45 N N N 0 3.645 -5.828 0.422
90 H46 H H46 N N N 0 5.294 -5.733 1.074



X6T : Chemical Bonds

Total Number of Bonds: 93
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F1 C16 F C sing 1.4 N N
2 F3 C16 F C sing 1.4 N N
3 C16 F2 C F sing 1.4 N N
4 C16 C15 C C sing 1.51 N N
5 C13 C11 C C sing 1.53 N N
6 C15 O2 C O doub 1.21 N N
7 C15 N2 C N sing 1.35 N N
8 C12 C11 C C sing 1.53 N N
9 N2 C10 N C sing 1.47 N N
10 C11 C10 C C sing 1.53 N N
11 C11 C14 C C sing 1.53 N N
12 C10 C9 C C sing 1.51 N N
13 C29 C28 C C sing 1.53 N N
14 C29 N5 C N sing 1.46 N N
15 C28 C27 C C sing 1.53 N N
16 N5 C30 N C sing 1.33 N N
17 O3 C9 O C doub 1.21 N N
18 C9 N1 C N sing 1.35 N N
19 C30 O6 C O doub 1.21 N N
20 C30 C26 C C sing 1.5 N N
21 N1 C8 N C sing 1.48 N N
22 N1 C2 N C sing 1.48 N N
23 C8 C4 C C sing 1.54 N N
24 C27 C26 C C sing 1.53 N N
25 C26 C25 C C sing 1.53 N N
26 C6 C5 C C sing 1.53 N N
27 C2 C1 C C sing 1.51 N N
28 C2 C3 C C sing 1.54 N N
29 O1 C1 O C doub 1.21 N N
30 C4 C5 C C sing 1.53 N N
31 C4 C3 C C sing 1.54 N N
32 C1 N3 C N sing 1.35 N N
33 C25 C17 C C sing 1.53 N N
34 C5 C3 C C sing 1.53 N N
35 C5 C7 C C sing 1.53 N N
36 N3 C17 N C sing 1.47 N N
37 C17 C18 C C sing 1.53 N N
38 C18 O5 C O sing 1.43 N N
39 C18 C19 C C sing 1.51 N N
40 C22 C21 C C sing 1.53 N N
41 O4 C19 O C doub 1.21 N N
42 C19 N4 C N sing 1.35 N N
43 N4 C20 N C sing 1.48 N N
44 N4 C24 N C sing 1.48 N N
45 C20 C21 C C sing 1.54 N N
46 C21 C24 C C sing 1.54 N N
47 C21 C23 C C sing 1.53 N N
48 N3 H1 N H sing 0.97 N N
49 C4 H2 C H sing 1.09 N N
50 C6 H3 C H sing 1.09 N N
51 C6 H4 C H sing 1.09 N N
52 C6 H5 C H sing 1.09 N N
53 C7 H6 C H sing 1.09 N N
54 C7 H7 C H sing 1.09 N N
55 C7 H8 C H sing 1.09 N N
56 C8 H9 C H sing 1.09 N N
57 C8 H10 C H sing 1.09 N N
58 C10 H11 C H sing 1.09 N N
59 C13 H12 C H sing 1.09 N N
60 C13 H13 C H sing 1.09 N N
61 C13 H14 C H sing 1.09 N N
62 C17 H15 C H sing 1.09 N N
63 C20 H16 C H sing 1.09 N N
64 C20 H17 C H sing 1.09 N N
65 C22 H18 C H sing 1.09 N N
66 C22 H19 C H sing 1.09 N N
67 C22 H20 C H sing 1.09 N N
68 C24 H21 C H sing 1.09 N N
69 C24 H22 C H sing 1.09 N N
70 C26 H23 C H sing 1.09 N N
71 C28 H24 C H sing 1.09 N N
72 C28 H25 C H sing 1.09 N N
73 C2 H26 C H sing 1.09 N N
74 N2 H27 N H sing 0.97 N N
75 C3 H28 C H sing 1.09 N N
76 N5 H29 N H sing 0.97 N N
77 O5 H30 O H sing 0.97 N N
78 C12 H31 C H sing 1.09 N N
79 C12 H32 C H sing 1.09 N N
80 C12 H33 C H sing 1.09 N N
81 C14 H34 C H sing 1.09 N N
82 C14 H35 C H sing 1.09 N N
83 C14 H36 C H sing 1.09 N N
84 C18 H37 C H sing 1.09 N N
85 C23 H38 C H sing 1.09 N N
86 C23 H39 C H sing 1.09 N N
87 C23 H40 C H sing 1.09 N N
88 C25 H41 C H sing 1.09 N N
89 C25 H42 C H sing 1.09 N N
90 C27 H43 C H sing 1.09 N N
91 C27 H44 C H sing 1.09 N N
92 C29 H45 C H sing 1.09 N N
93 C29 H46 C H sing 1.09 N N



X6T : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
X6T 8f02 Open in New Window Bound ligand 1 1