Chemical Components in the PDB

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XO7 : Summary

Code

XO7

One-letter code

X

Molecule name

(5S)-4-({1-[(4-bromophenyl)methyl]-1H-imidazol-5-yl}methyl)-5-propyl-1-[3-(trifluoromethoxy)phenyl]piperazin-2-one

Systematic names

ProgramVersionName
ACDLabs 12.01 (5S)-4-({1-[(4-bromophenyl)methyl]-1H-imidazol-5-yl}methyl)-5-propyl-1-[3-(trifluoromethoxy)phenyl]piperazin-2-one
OpenEye OEToolkits 2.0.7 (5~{S})-4-[[3-[(4-bromophenyl)methyl]imidazol-4-yl]methyl]-5-propyl-1-[3-(trifluoromethyloxy)phenyl]piperazin-2-one

Formula

C25 H26 Br F3 N4 O2

Formal charge

0

Molecular weight

551.399 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c1ccc(cc1OC(F)(F)F)N2CC(CCC)N(CC2=O)Cc4cncn4Cc3ccc(Br)cc3
SMILES CACTVS 3.385 CCC[CH]1CN(C(=O)CN1Cc2cncn2Cc3ccc(Br)cc3)c4cccc(OC(F)(F)F)c4
SMILES OpenEye OEToolkits 2.0.7 CCCC1CN(C(=O)CN1Cc2cncn2Cc3ccc(cc3)Br)c4cccc(c4)OC(F)(F)F
Canonical SMILES CACTVS 3.385 CCC[C@H]1CN(C(=O)CN1Cc2cncn2Cc3ccc(Br)cc3)c4cccc(OC(F)(F)F)c4
Canonical SMILES OpenEye OEToolkits 2.0.7 CCC[C@H]1CN(C(=O)CN1Cc2cncn2Cc3ccc(cc3)Br)c4cccc(c4)OC(F)(F)F

IUPAC InChI

InChI=1S/C25H26BrF3N4O2/c1-2-4-21-15-33(20-5-3-6-23(11-20)35-25(27,28)29)24(34)16-31(21)14-22-12-30-17-32(22)13-18-7-9-19(26)10-8-18/h3,5-12,17,21H,2,4,13-16H2,1H3/t21-/m0/s1

IUPAC InChI key

MMOUEYPUGKAJHU-NRFANRHFSA-N
XO7

wwPDB Information

Atom count

61 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-12-22

Last modified at

2022-11-04

Status

Released

Obsoleted

Not Assigned



XO7 : Atoms of Molecule

Total Number of Atoms: 61
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N Y N 0 5.021 2.105 0.221
2 C13 C C2 N N N 0 7.669 1.599 0.04
3 C17 C C3 N Y N 0 4.486 -0.192 -0.23
4 C20 C C4 N N N 0 1.12 -3.01 0.487
5 C22 C C5 N N N 0 -0.862 -1.694 0.03
6 C24 C C6 N Y N 0 -2.076 -3.651 1.126
7 C26 C C7 N Y N 0 -3.086 -2.67 2.762
8 C28 C C8 N N N 0 -2.331 -0.296 2.423
9 C01 C C9 N N N 0 -1.926 -3.376 -4.313
10 C02 C C10 N N N 0 -0.947 -3.478 -3.142
11 C03 C C11 N N N 0 -0.371 -2.093 -2.837
12 C04 C C12 S N N 0 0.699 -2.214 -1.75
13 C05 C C13 N N N 0 1.329 -0.847 -1.499
14 C29 C C20 N Y N 0 -3.371 0.444 1.622
15 C07 C C14 N Y N 0 3.135 0.106 -0.13
16 C08 C C15 N Y N 0 2.731 1.406 0.151
17 C09 C C16 N Y N 0 3.674 2.401 0.32
18 C11 C C17 N Y N 0 5.429 0.808 -0.055
19 C18 C C18 N N N 0 2.086 -1.866 0.607
20 C23 C C19 N Y N 0 -1.753 -2.345 1.056
21 C30 C C21 N Y N 0 -4.643 0.618 2.135
22 C31 C C22 N Y N 0 -5.597 1.297 1.401
23 C32 C C23 N Y N 0 -5.279 1.803 0.153
24 C34 C C24 N Y N 0 -4.006 1.63 -0.359
25 C35 C C25 N Y N 0 -3.051 0.955 0.378
26 F14 F F1 N N N 0 8.98 1.128 -0.094
27 F15 F F2 N N N 0 7.496 2.136 1.32
28 F16 F F3 N N N 0 7.43 2.59 -0.918
29 N06 N N1 N N N 0 2.18 -0.9 -0.313
30 N21 N N2 N N N 0 0.081 -2.687 -0.5
31 N25 N N3 N Y N 0 -2.891 -3.82 2.178
32 N27 N N4 N Y N 0 -2.389 -1.724 2.097
33 O12 O O1 N N N 0 6.754 0.519 -0.152
34 O19 O O2 N N N 0 2.81 -1.816 1.578
35 BR33 BR BR1 N N N 0 -6.584 2.733 -0.852
36 H1 H H1 N N N 0 5.755 2.886 0.353
37 H2 H H2 N N N 0 4.802 -1.202 -0.449
38 H3 H H3 N N N 0 1.656 -3.905 0.169
39 H4 H H4 N N N 0 0.654 -3.194 1.456
40 H5 H H5 N N N 0 -1.472 -1.301 -0.784
41 H6 H H6 N N N 0 -0.308 -0.879 0.495
42 H7 H H7 N N N 0 -1.742 -4.424 0.451
43 H8 H H8 N N N 0 -3.697 -2.503 3.637
44 H9 H H9 N N N 0 -1.342 0.092 2.181
45 H10 H H10 N N N 0 -2.526 -0.158 3.487
46 H11 H H11 N N N 0 -2.736 -2.695 -4.052
47 H12 H H12 N N N 0 -1.403 -2.998 -5.192
48 H13 H H13 N N N 0 -2.336 -4.362 -4.531
49 H14 H H14 N N N 0 -1.47 -3.855 -2.263
50 H15 H H15 N N N 0 -0.137 -4.158 -3.404
51 H16 H H16 N N N 0 0.075 -1.678 -3.741
52 H17 H H17 N N N 0 -1.169 -1.436 -2.49
53 H23 H H23 N N N 0 -4.892 0.222 3.108
54 H18 H H18 N N N 0 1.466 -2.92 -2.069
55 H19 H H19 N N N 0 1.932 -0.563 -2.361
56 H20 H H20 N N N 0 0.543 -0.108 -1.35
57 H21 H H21 N N N 0 1.68 1.64 0.229
58 H22 H H22 N N N 0 3.359 3.412 0.53
59 H24 H H24 N N N 0 -6.591 1.432 1.801
60 H25 H H25 N N N 0 -3.757 2.024 -1.333
61 H26 H H26 N N N 0 -2.057 0.819 -0.022



XO7 : Chemical Bonds

Total Number of Bonds: 64
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C01 C02 C C sing 1.53 N N
2 F14 C13 F C sing 1.4 N N
3 C02 C03 C C sing 1.53 N N
4 F16 C13 F C sing 1.4 N N
5 C13 O12 C O sing 1.43 N N
6 C13 F15 C F sing 1.4 N N
7 C03 C04 C C sing 1.53 N N
8 N25 C24 N C sing 1.34 N Y
9 N25 C26 N C doub 1.3 N Y
10 O12 C11 O C sing 1.36 N N
11 C24 C23 C C doub 1.35 N Y
12 C05 C04 C C sing 1.53 N N
13 C05 N06 C N sing 1.46 N N
14 C11 C10 C C doub 1.39 N Y
15 C11 C17 C C sing 1.39 N Y
16 C10 C09 C C sing 1.38 N Y
17 C04 N21 C N sing 1.47 N N
18 C17 C07 C C doub 1.39 N Y
19 C09 C08 C C doub 1.38 N Y
20 C07 C08 C C sing 1.39 N Y
21 C07 N06 C N sing 1.4 N N
22 C26 N27 C N sing 1.35 N Y
23 N06 C18 N C sing 1.34 N N
24 C23 C22 C C sing 1.51 N N
25 C23 N27 C N sing 1.37 N Y
26 N21 C22 N C sing 1.47 N N
27 N21 C20 N C sing 1.47 N N
28 N27 C28 N C sing 1.47 N N
29 C35 C34 C C doub 1.38 N Y
30 C35 C29 C C sing 1.38 N Y
31 C34 C32 C C sing 1.38 N Y
32 C18 C20 C C sing 1.5 N N
33 C18 O19 C O doub 1.21 N N
34 C28 C29 C C sing 1.51 N N
35 C29 C30 C C doub 1.38 N Y
36 C32 BR33 C BR sing 1.89 N N
37 C32 C31 C C doub 1.38 N Y
38 C30 C31 C C sing 1.38 N Y
39 C10 H1 C H sing 1.08 N N
40 C17 H2 C H sing 1.08 N N
41 C20 H3 C H sing 1.09 N N
42 C20 H4 C H sing 1.09 N N
43 C22 H5 C H sing 1.09 N N
44 C22 H6 C H sing 1.09 N N
45 C24 H7 C H sing 1.08 N N
46 C26 H8 C H sing 1.08 N N
47 C28 H9 C H sing 1.09 N N
48 C28 H10 C H sing 1.09 N N
49 C01 H11 C H sing 1.09 N N
50 C01 H12 C H sing 1.09 N N
51 C01 H13 C H sing 1.09 N N
52 C02 H14 C H sing 1.09 N N
53 C02 H15 C H sing 1.09 N N
54 C03 H16 C H sing 1.09 N N
55 C03 H17 C H sing 1.09 N N
56 C04 H18 C H sing 1.09 N N
57 C05 H19 C H sing 1.09 N N
58 C05 H20 C H sing 1.09 N N
59 C08 H21 C H sing 1.08 N N
60 C09 H22 C H sing 1.08 N N
61 C30 H23 C H sing 1.08 N N
62 C31 H24 C H sing 1.08 N N
63 C34 H25 C H sing 1.08 N N
64 C35 H26 C H sing 1.08 N N



XO7 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XO7 7t0d Open in New Window Bound ligand 1 1