Chemical Components in the PDB

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5TB : Summary

Code

5TB

One-letter code

X

Molecule name

3-cyclopentyl-1-[3-[4-(methylaminomethyl)phenyl]-1,3-diazinan-1-yl]propan-1-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.4 3-cyclopentyl-1-[3-[4-(methylaminomethyl)phenyl]-1,3-diazinan-1-yl]propan-1-one

Formula

C20 H31 N3 O

Formal charge

0

Molecular weight

329.48 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CNCc1ccc(cc1)N2CCCN(C2)C(=O)CCC3CCCC3
SMILES OpenEye OEToolkits 2.0.4 CNCc1ccc(cc1)N2CCCN(C2)C(=O)CCC3CCCC3
Canonical SMILES CACTVS 3.385 CNCc1ccc(cc1)N2CCCN(C2)C(=O)CCC3CCCC3
Canonical SMILES OpenEye OEToolkits 2.0.4 CNCc1ccc(cc1)N2CCCN(C2)C(=O)CCC3CCCC3

IUPAC InChI

InChI=1S/C20H31N3O/c1-21-15-18-7-10-19(11-8-18)22-13-4-14-23(16-22)20(24)12-9-17-5-2-3-6-17/h7-8,10-11,17,21H,2-6,9,12-16H2,1H3

IUPAC InChI key

FGLHMHLKBALILM-UHFFFAOYSA-N
5TB

wwPDB Information

Atom count

55 (24 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-11-27

Last modified at

2016-01-29

Status

Released

Obsoleted

Not Assigned



5TB : 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 C1 C C1 N N N 0 -5.706 -0.399 -0.646
2 C2 C C2 N N N 0 -6.293 0.174 0.66
3 C3 C C3 N N N 0 -7.78 -0.259 0.629
4 O O O1 N N N 0 -1.707 -1.359 0.058
5 C7 C C4 N N N 0 -1.959 -0.173 0.11
6 C6 C C5 N N N 0 -3.367 0.309 -0.126
7 C5 C C6 N N N 0 -4.276 -0.889 -0.407
8 C4 C C7 N N N 0 -7.709 -1.681 0.02
9 C C C8 N N N 0 -6.606 -1.579 -1.053
10 N N N1 N N N 0 -0.979 0.712 0.378
11 C11 C C9 N N N 0 0.4 0.261 0.611
12 N1 N N2 N N N 0 1.301 1.008 -0.279
13 C10 C C10 N N N 0 1.156 2.456 -0.082
14 C9 C C11 N N N 0 -0.264 2.886 -0.458
15 C8 C C12 N N N 0 -1.263 2.154 0.439
16 C12 C C13 N Y N 0 2.627 0.609 -0.099
17 C17 C C14 N Y N 0 2.937 -0.381 0.825
18 C16 C C15 N Y N 0 4.249 -0.774 1.0
19 C15 C C16 N Y N 0 5.254 -0.183 0.257
20 C14 C C17 N Y N 0 4.95 0.803 -0.664
21 C13 C C18 N Y N 0 3.639 1.196 -0.848
22 C18 C C19 N N N 0 6.686 -0.613 0.452
23 N2 N N3 N N N 0 6.993 -1.719 -0.466
24 C19 C C20 N N N 0 8.383 -2.166 -0.304
25 H1 H H1 N N N 0 -5.713 0.363 -1.426
26 H2 H H2 N N N 0 -5.789 -0.254 1.526
27 H3 H H3 N N N 0 -6.211 1.261 0.67
28 H4 H H4 N N N 0 -8.194 -0.29 1.637
29 H5 H H5 N N N 0 -8.363 0.406 -0.008
30 H6 H H6 N N N 0 -3.723 0.836 0.759
31 H7 H H7 N N N 0 -3.381 0.985 -0.981
32 H8 H H8 N N N 0 -4.262 -1.564 0.448
33 H9 H H9 N N N 0 -3.92 -1.416 -1.292
34 H10 H H10 N N N 0 -7.434 -2.409 0.783
35 H14 H H14 N N N 0 0.675 0.447 1.649
36 H11 H H11 N N N 0 -8.662 -1.948 -0.437
37 H12 H H12 N N N 0 -7.051 -1.389 -2.03
38 H13 H H13 N N N 0 -6.024 -2.5 -1.08
39 H15 H H15 N N N 0 0.476 -0.806 0.398
40 H16 H H16 N N N 0 1.345 2.701 0.963
41 H17 H H17 N N N 0 1.873 2.982 -0.713
42 H18 H H18 N N N 0 -0.371 3.962 -0.32
43 H19 H H19 N N N 0 -0.454 2.631 -1.5
44 H20 H H20 N N N 0 -2.278 2.344 0.09
45 H21 H H21 N N N 0 -1.157 2.501 1.467
46 H22 H H22 N N N 0 2.152 -0.842 1.406
47 H23 H H23 N N N 0 4.491 -1.543 1.719
48 H24 H H24 N N N 0 5.737 1.262 -1.243
49 H25 H H25 N N N 0 3.401 1.963 -1.571
50 H26 H H26 N N N 0 7.349 0.226 0.244
51 H27 H H27 N N N 0 6.829 -0.944 1.48
52 H32 H H32 N N N 0 8.538 -2.507 0.72
53 H28 H H28 N N N 0 6.806 -1.458 -1.422
54 H30 H H30 N N N 0 8.584 -2.985 -0.995
55 H31 H H31 N N N 0 9.059 -1.337 -0.516



5TB : Chemical Bonds

Total Number of Bonds: 57
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C3 C2 C C sing 1.55 N N
2 C3 C4 C C sing 1.55 N N
3 C2 C1 C C sing 1.54 N N
4 C4 C C C sing 1.54 N N
5 C9 C8 C C sing 1.53 N N
6 C9 C10 C C sing 1.53 N N
7 C8 N C N sing 1.47 N N
8 C6 C5 C C sing 1.53 N N
9 C6 C7 C C sing 1.51 N N
10 C1 C C C sing 1.54 N N
11 C1 C5 C C sing 1.53 N N
12 C10 N1 C N sing 1.47 N N
13 N C7 N C sing 1.35 N N
14 N C11 N C sing 1.47 N N
15 C7 O C O doub 1.21 N N
16 N1 C11 N C sing 1.47 N N
17 N1 C12 N C sing 1.4 N N
18 C17 C12 C C doub 1.39 N Y
19 C17 C16 C C sing 1.38 N Y
20 C12 C13 C C sing 1.39 N Y
21 C16 C15 C C doub 1.38 N Y
22 C13 C14 C C doub 1.38 N Y
23 C15 C14 C C sing 1.38 N Y
24 C15 C18 C C sing 1.51 N N
25 C19 N2 C N sing 1.47 N N
26 C18 N2 C N sing 1.47 N N
27 C1 H1 C H sing 1.09 N N
28 C2 H2 C H sing 1.09 N N
29 C2 H3 C H sing 1.09 N N
30 C3 H4 C H sing 1.09 N N
31 C3 H5 C H sing 1.09 N N
32 C6 H6 C H sing 1.09 N N
33 C6 H7 C H sing 1.09 N N
34 C5 H8 C H sing 1.09 N N
35 C5 H9 C H sing 1.09 N N
36 C4 H10 C H sing 1.09 N N
37 C4 H11 C H sing 1.09 N N
38 C H12 C H sing 1.09 N N
39 C H13 C H sing 1.09 N N
40 C11 H14 C H sing 1.09 N N
41 C11 H15 C H sing 1.09 N N
42 C10 H16 C H sing 1.09 N N
43 C10 H17 C H sing 1.09 N N
44 C9 H18 C H sing 1.09 N N
45 C9 H19 C H sing 1.09 N N
46 C8 H20 C H sing 1.09 N N
47 C8 H21 C H sing 1.09 N N
48 C17 H22 C H sing 1.08 N N
49 C16 H23 C H sing 1.08 N N
50 C14 H24 C H sing 1.08 N N
51 C13 H25 C H sing 1.08 N N
52 C18 H26 C H sing 1.09 N N
53 C18 H27 C H sing 1.09 N N
54 N2 H28 N H sing 1.01 N N
55 C19 H30 C H sing 1.09 N N
56 C19 H31 C H sing 1.09 N N
57 C19 H32 C H sing 1.09 N N



5TB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5TB 5f04 Open in New Window Bound ligand 1 1