Chemical Components in the PDB

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XOA : Summary

Code

XOA

One-letter code

X

Molecule name

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

Systematic names

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

Formula

C25 H28 Br Cl N4 O

Formal charge

0

Molecular weight

515.873 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c4cc(N1C(CN(C(CCCC)C1)Cc2n(cnc2)Cc3ccc(Br)cc3)=O)cc(c4)Cl
SMILES CACTVS 3.385 CCCC[CH]1CN(C(=O)CN1Cc2cncn2Cc3ccc(Br)cc3)c4cccc(Cl)c4
SMILES OpenEye OEToolkits 2.0.7 CCCCC1CN(C(=O)CN1Cc2cncn2Cc3ccc(cc3)Br)c4cccc(c4)Cl
Canonical SMILES CACTVS 3.385 CCCC[C@H]1CN(C(=O)CN1Cc2cncn2Cc3ccc(Br)cc3)c4cccc(Cl)c4
Canonical SMILES OpenEye OEToolkits 2.0.7 CCCC[C@H]1CN(C(=O)CN1Cc2cncn2Cc3ccc(cc3)Br)c4cccc(c4)Cl

IUPAC InChI

InChI=1S/C25H28BrClN4O/c1-2-3-6-23-16-31(22-7-4-5-21(27)12-22)25(32)17-29(23)15-24-13-28-18-30(24)14-19-8-10-20(26)11-9-19/h4-5,7-13,18,23H,2-3,6,14-17H2,1H3/t23-/m0/s1

IUPAC InChI key

DJAYAIKODCJWBJ-QHCPKHFHSA-N
XOA

wwPDB Information

Atom count

60 (32 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



XOA : Atoms of Molecule

Total Number of Atoms: 60
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 4.134 3.401 -0.361
2 C15 C C2 N N N 0 3.139 -0.855 0.958
3 C17 C C3 N N N 0 2.333 -2.108 1.147
4 C20 C C4 N Y N 0 -0.592 -1.701 1.704
5 C21 C C5 N Y N 0 -0.707 -2.984 2.098
6 C26 C C6 N Y N 0 -2.616 0.861 1.628
7 C28 C C7 N Y N 0 -4.95 1.242 1.255
8 C01 C C8 N N N 0 -1.173 -5.419 -3.19
9 C02 C C9 N N N 0 -0.764 -3.946 -3.257
10 C03 C C10 N N N 0 0.245 -3.646 -2.147
11 C04 C C11 N N N 0 0.655 -2.174 -2.214
12 C05 C C12 S N N 0 1.755 -1.903 -1.186
13 C06 C C13 N N N 0 2.197 -0.438 -1.274
14 C08 C C14 N Y N 0 3.894 1.017 -0.251
15 C09 C C15 N Y N 0 3.326 2.284 -0.266
16 C11 C C16 N Y N 0 5.507 3.258 -0.446
17 C12 C C17 N Y N 0 6.076 1.996 -0.437
18 C14 C C18 N Y N 0 5.272 0.875 -0.342
19 C19 C C19 N N N 0 0.178 -1.193 0.512
20 C23 C C20 N Y N 0 -1.839 -1.796 3.5
21 C25 C C21 N N N 0 -1.484 0.507 2.558
22 C27 C C22 N Y N 0 -3.912 0.917 2.108
23 C29 C C23 N Y N 0 -4.693 1.511 -0.077
24 C31 C C24 N Y N 0 -3.395 1.465 -0.553
25 C32 C C25 N Y N 0 -2.358 1.134 0.298
26 N07 N N1 N N N 0 3.078 -0.116 -0.155
27 O16 O O1 N N N 0 3.872 -0.495 1.855
28 N18 N N2 N N N 0 1.237 -2.152 0.169
29 N22 N N3 N Y N 0 -1.475 -3.012 3.198
30 N24 N N4 N Y N 0 -1.315 -0.948 2.589
31 BR30 BR BR1 N N N 0 -6.114 1.956 -1.243
32 CL13 CL CL1 N N N 0 7.799 1.821 -0.545
33 H1 H H1 N N N 0 3.692 4.386 -0.373
34 H2 H H2 N N N 0 2.977 -2.977 1.008
35 H3 H H3 N N N 0 1.917 -2.123 2.154
36 H4 H H4 N N N 0 -0.26 -3.839 1.614
37 H5 H H5 N N N 0 -5.962 1.286 1.63
38 H6 H H6 N N N 0 -1.892 -5.632 -3.981
39 H7 H H7 N N N 0 -0.292 -6.047 -3.321
40 H8 H H8 N N N 0 -1.627 -5.626 -2.221
41 H9 H H9 N N N 0 -0.31 -3.739 -4.226
42 H10 H H10 N N N 0 -1.645 -3.318 -3.127
43 H11 H H11 N N N 0 -0.209 -3.854 -1.178
44 H12 H H12 N N N 0 1.126 -4.275 -2.277
45 H13 H H13 N N N 0 1.026 -1.945 -3.213
46 H14 H H14 N N N 0 -0.209 -1.546 -1.995
47 H15 H H15 N N N 0 2.605 -2.559 -1.379
48 H16 H H16 N N N 0 2.735 -0.278 -2.208
49 H17 H H17 N N N 0 1.319 0.207 -1.25
50 H18 H H18 N N N 0 2.254 2.397 -0.203
51 H19 H H19 N N N 0 6.136 4.132 -0.521
52 H23 H H23 N N N 0 -2.463 -1.516 4.336
53 H20 H H20 N N N 0 5.716 -0.109 -0.335
54 H21 H H21 N N N 0 -0.497 -1.079 -0.335
55 H22 H H22 N N N 0 0.626 -0.229 0.753
56 H24 H H24 N N N 0 -0.564 0.972 2.204
57 H25 H H25 N N N 0 -1.711 0.868 3.561
58 H26 H H26 N N N 0 -4.112 0.707 3.148
59 H27 H H27 N N N 0 -3.193 1.682 -1.592
60 H28 H H28 N N N 0 -1.346 1.09 -0.076



XOA : Chemical Bonds

Total Number of Bonds: 63
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 C02 C03 C C sing 1.53 N N
3 C03 C04 C C sing 1.53 N N
4 C04 C05 C C sing 1.53 N N
5 N22 C21 N C sing 1.34 N Y
6 N22 C23 N C doub 1.3 N Y
7 C21 C20 C C doub 1.35 N Y
8 CL13 C12 CL C sing 1.74 N N
9 C06 C05 C C sing 1.53 N N
10 C06 N07 C N sing 1.46 N N
11 C05 N18 C N sing 1.47 N N
12 C12 C11 C C doub 1.38 N Y
13 C12 C14 C C sing 1.38 N Y
14 C11 C10 C C sing 1.38 N Y
15 C14 C08 C C doub 1.39 N Y
16 C10 C09 C C doub 1.38 N Y
17 C08 C09 C C sing 1.39 N Y
18 C08 N07 C N sing 1.4 N N
19 C23 N24 C N sing 1.35 N Y
20 N07 C15 N C sing 1.34 N N
21 C20 C19 C C sing 1.51 N N
22 C20 N24 C N sing 1.37 N Y
23 N18 C19 N C sing 1.47 N N
24 N18 C17 N C sing 1.47 N N
25 N24 C25 N C sing 1.47 N N
26 C32 C31 C C doub 1.38 N Y
27 C32 C26 C C sing 1.38 N Y
28 C31 C29 C C sing 1.38 N Y
29 C15 C17 C C sing 1.5 N N
30 C15 O16 C O doub 1.21 N N
31 C25 C26 C C sing 1.51 N N
32 C26 C27 C C doub 1.38 N Y
33 C29 BR30 C BR sing 1.89 N N
34 C29 C28 C C doub 1.38 N Y
35 C27 C28 C C sing 1.38 N Y
36 C10 H1 C H sing 1.08 N N
37 C17 H2 C H sing 1.09 N N
38 C17 H3 C H sing 1.09 N N
39 C21 H4 C H sing 1.08 N N
40 C28 H5 C H sing 1.08 N N
41 C01 H6 C H sing 1.09 N N
42 C01 H7 C H sing 1.09 N N
43 C01 H8 C H sing 1.09 N N
44 C02 H9 C H sing 1.09 N N
45 C02 H10 C H sing 1.09 N N
46 C03 H11 C H sing 1.09 N N
47 C03 H12 C H sing 1.09 N N
48 C04 H13 C H sing 1.09 N N
49 C04 H14 C H sing 1.09 N N
50 C05 H15 C H sing 1.09 N N
51 C06 H16 C H sing 1.09 N N
52 C06 H17 C H sing 1.09 N N
53 C09 H18 C H sing 1.08 N N
54 C11 H19 C H sing 1.08 N N
55 C14 H20 C H sing 1.08 N N
56 C19 H21 C H sing 1.09 N N
57 C19 H22 C H sing 1.09 N N
58 C23 H23 C H sing 1.08 N N
59 C25 H24 C H sing 1.09 N N
60 C25 H25 C H sing 1.09 N N
61 C27 H26 C H sing 1.08 N N
62 C31 H27 C H sing 1.08 N N
63 C32 H28 C H sing 1.08 N N



XOA : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XOA 7t0e Open in New Window Bound ligand 1 1