Chemical Components in the PDB

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5XI : Summary

Code

5XI

One-letter code

X

Molecule name

methyl 4-[4-(3-methyl-2-oxidanylidene-benzimidazol-1-yl)piperidin-1-yl]piperidine-1-carboxylate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 methyl 4-[4-(3-methyl-2-oxidanylidene-benzimidazol-1-yl)piperidin-1-yl]piperidine-1-carboxylate

Formula

C20 H28 N4 O3

Formal charge

0

Molecular weight

372.461 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COC(=O)N1CCC(CC1)N2CCC(CC2)N3C(=O)N(C)c4ccccc34
SMILES OpenEye OEToolkits 2.0.7 CN1c2ccccc2N(C1=O)C3CCN(CC3)C4CCN(CC4)C(=O)OC
Canonical SMILES CACTVS 3.385 COC(=O)N1CCC(CC1)N2CCC(CC2)N3C(=O)N(C)c4ccccc34
Canonical SMILES OpenEye OEToolkits 2.0.7 CN1c2ccccc2N(C1=O)C3CCN(CC3)C4CCN(CC4)C(=O)OC

IUPAC InChI

InChI=1S/C20H28N4O3/c1-21-17-5-3-4-6-18(17)24(19(21)25)16-9-11-22(12-10-16)15-7-13-23(14-8-15)20(26)27-2/h3-6,15-16H,7-14H2,1-2H3

IUPAC InChI key

LFVHMTNJDWYMGD-UHFFFAOYSA-N
5XI

wwPDB Information

Atom count

55 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-08-25

Last modified at

2022-05-06

Status

Released

Obsoleted

Not Assigned



5XI : Atoms of Molecule

Total Number of Atoms: 55
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C14 C C1 N N N 0 -1.678 1.758 0.01
2 C13 C C2 N N N 0 1.899 2.91 -0.226
3 C12 C C3 N N N 0 0.601 2.451 0.442
4 C16 C C4 N N N 0 -4.064 1.198 -0.472
5 C17 C C5 N N N 0 -2.9 0.213 1.545
6 C19 C C6 N N N 0 -4.698 -0.998 0.407
7 C20 C C7 N N N 0 -6.431 -2.297 -0.594
8 C11 C C8 N N N 0 0.117 0.95 -1.397
9 C8 C C9 N N N 0 3.36 -0.968 2.962
10 C6 C C10 N Y N 0 3.047 -0.668 -0.675
11 C7 C C11 N N N 0 2.86 0.641 1.11
12 C2 C C12 N Y N 0 3.404 -2.595 -2.052
13 C5 C C13 N Y N 0 3.303 -1.438 0.462
14 C4 C C14 N Y N 0 3.609 -2.784 0.33
15 C3 C C15 N Y N 0 3.658 -3.358 -0.925
16 C1 C C16 N Y N 0 3.105 -1.253 -1.931
17 C10 C C17 N N N 0 1.401 1.364 -2.12
18 C15 C C18 N N N 0 -2.698 1.491 -1.099
19 C18 C C19 N N N 0 -1.547 0.517 0.895
20 C9 C C20 N N N 0 2.454 1.772 -1.086
21 N1 N N1 N N N 0 3.177 -0.589 1.559
22 N2 N N2 N N N 0 2.774 0.624 -0.234
23 N3 N N3 N N N 0 -0.374 2.072 -0.588
24 N4 N N4 N N N 0 -3.916 0.097 0.49
25 O1 O O1 N N N 0 2.678 1.618 1.812
26 O2 O O2 N N N 0 -4.567 -1.901 1.209
27 O3 O O3 N N N 0 -5.625 -1.09 -0.565
28 H1 H H1 N N N 0 -2.013 2.602 0.615
29 H2 H H2 N N N 0 1.698 3.777 -0.855
30 H3 H H3 N N N 0 2.628 3.177 0.54
31 H4 H H4 N N N 0 0.805 1.592 1.082
32 H5 H H5 N N N 0 0.195 3.264 1.045
33 H6 H H6 N N N 0 -4.428 2.087 0.043
34 H7 H H7 N N N 0 -4.77 0.912 -1.251
35 H8 H H8 N N N 0 -2.838 -0.725 2.097
36 H9 H H9 N N N 0 -3.171 1.02 2.226
37 H10 H H10 N N N 0 -7.137 -2.243 -1.424
38 H11 H H11 N N N 0 -5.783 -3.164 -0.724
39 H12 H H12 N N N 0 -6.98 -2.391 0.343
40 H13 H H13 N N N 0 -0.639 0.672 -2.131
41 H14 H H14 N N N 0 0.324 0.098 -0.749
42 H15 H H15 N N N 0 4.404 -0.828 3.243
43 H16 H H16 N N N 0 2.727 -0.344 3.592
44 H17 H H17 N N N 0 3.085 -2.014 3.094
45 H18 H H18 N N N 0 3.45 -3.05 -3.03
46 H19 H H19 N N N 0 3.807 -3.382 1.207
47 H20 H H20 N N N 0 3.896 -4.406 -1.027
48 H21 H H21 N N N 0 2.913 -0.66 -2.813
49 H22 H H22 N N N 0 1.774 0.525 -2.708
50 H23 H H23 N N N 0 1.192 2.206 -2.78
51 H24 H H24 N N N 0 -2.773 2.367 -1.743
52 H25 H H25 N N N 0 -2.376 0.632 -1.689
53 H26 H H26 N N N 0 -1.236 -0.333 0.287
54 H27 H H27 N N N 0 -0.804 0.7 1.671
55 H28 H H28 N N N 0 3.356 2.109 -1.598



5XI : Chemical Bonds

Total Number of Bonds: 58
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C8 N1 C N sing 1.46 N N
2 C4 C3 C C doub 1.38 N Y
3 C4 C5 C C sing 1.39 N Y
4 N1 C5 N C sing 1.39 N N
5 N1 C7 N C sing 1.35 N N
6 C3 C2 C C sing 1.38 N Y
7 C5 C6 C C doub 1.4 N Y
8 C7 O1 C O doub 1.22 N N
9 C7 N2 C N sing 1.35 N N
10 C2 C1 C C doub 1.38 N Y
11 C6 N2 C N sing 1.39 N N
12 C6 C1 C C sing 1.39 N Y
13 N2 C9 N C sing 1.46 N N
14 C9 C13 C C sing 1.53 N N
15 C9 C10 C C sing 1.53 N N
16 C13 C12 C C sing 1.53 N N
17 C10 C11 C C sing 1.53 N N
18 C12 N3 C N sing 1.47 N N
19 C11 N3 C N sing 1.47 N N
20 N3 C14 N C sing 1.47 N N
21 C18 C14 C C sing 1.53 N N
22 C18 C17 C C sing 1.53 N N
23 C14 C15 C C sing 1.53 N N
24 C15 C16 C C sing 1.53 N N
25 C17 N4 C N sing 1.47 N N
26 N4 C16 N C sing 1.47 N N
27 N4 C19 N C sing 1.35 N N
28 O3 C19 O C sing 1.35 N N
29 O3 C20 O C sing 1.45 N N
30 C19 O2 C O doub 1.21 N N
31 C14 H1 C H sing 1.09 N N
32 C13 H2 C H sing 1.09 N N
33 C13 H3 C H sing 1.09 N N
34 C12 H4 C H sing 1.09 N N
35 C12 H5 C H sing 1.09 N N
36 C16 H6 C H sing 1.09 N N
37 C16 H7 C H sing 1.09 N N
38 C17 H8 C H sing 1.09 N N
39 C17 H9 C H sing 1.09 N N
40 C20 H10 C H sing 1.09 N N
41 C20 H11 C H sing 1.09 N N
42 C20 H12 C H sing 1.09 N N
43 C11 H13 C H sing 1.09 N N
44 C11 H14 C H sing 1.09 N N
45 C8 H15 C H sing 1.09 N N
46 C8 H16 C H sing 1.09 N N
47 C8 H17 C H sing 1.09 N N
48 C2 H18 C H sing 1.08 N N
49 C4 H19 C H sing 1.08 N N
50 C3 H20 C H sing 1.08 N N
51 C1 H21 C H sing 1.08 N N
52 C10 H22 C H sing 1.09 N N
53 C10 H23 C H sing 1.09 N N
54 C15 H24 C H sing 1.09 N N
55 C15 H25 C H sing 1.09 N N
56 C18 H26 C H sing 1.09 N N
57 C18 H27 C H sing 1.09 N N
58 C9 H28 C H sing 1.09 N N



5XI : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5XI 7v6a Open in New Window Bound ligand 1 1