Chemical Components in the PDB

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5R8 : Summary

Code

5R8

One-letter code

X

Molecule name

[4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]methanamine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.4 [4-[(4-methyl-1,4-diazepan-1-yl)methyl]phenyl]methanamine

Formula

C14 H23 N3

Formal charge

0

Molecular weight

233.353 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1CCCN(CC1)Cc2ccc(CN)cc2
SMILES OpenEye OEToolkits 2.0.4 CN1CCCN(CC1)Cc2ccc(cc2)CN
Canonical SMILES CACTVS 3.385 CN1CCCN(CC1)Cc2ccc(CN)cc2
Canonical SMILES OpenEye OEToolkits 2.0.4 CN1CCCN(CC1)Cc2ccc(cc2)CN

IUPAC InChI

InChI=1S/C14H23N3/c1-16-7-2-8-17(10-9-16)12-14-5-3-13(11-15)4-6-14/h3-6H,2,7-12,15H2,1H3

IUPAC InChI key

AQLZGQUKWNQYPH-UHFFFAOYSA-N
5R8

wwPDB Information

Atom count

40 (17 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-11-16

Last modified at

2015-12-31

Status

Released

Obsoleted

Not Assigned



5R8 : Atoms of Molecule

Total Number of Atoms: 40
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C6 C C1 N N N 0 -2.213 -1.417 -0.28
2 C1 C C2 N N N 0 -4.472 -2.156 0.231
3 N2 N N1 N N N 0 -3.602 -0.993 0.012
4 C7 C C3 N N N 0 -1.471 -0.399 -1.019
5 N8 N N2 N N N 0 -1.364 0.872 -0.266
6 C9 C C4 N N N 0 -2.584 1.627 -0.402
7 C10 C C5 N N N 0 -3.57 1.376 0.759
8 C11 C C6 N N N 0 -3.617 -0.115 1.155
9 C22 C C7 N N N 0 -0.206 1.655 -0.718
10 C23 C C8 N Y N 0 1.064 0.923 -0.369
11 C26 C C9 N Y N 0 1.613 0.026 -1.265
12 C27 C C10 N Y N 0 2.778 -0.646 -0.945
13 C28 C C11 N Y N 0 3.393 -0.421 0.273
14 C29 C C12 N Y N 0 2.843 0.477 1.169
15 C30 C C13 N Y N 0 1.682 1.153 0.846
16 C35 C C14 N N N 0 4.662 -1.154 0.623
17 N36 N N3 N N N 0 5.82 -0.372 0.171
18 H1 H H1 N N N 0 -1.699 -1.617 0.66
19 H2 H H2 N N N 0 -2.239 -2.333 -0.87
20 H3 H H3 N N N 0 -4.099 -2.736 1.075
21 H4 H H4 N N N 0 -5.486 -1.817 0.443
22 H5 H H5 N N N 0 -4.478 -2.779 -0.664
23 H7 H H7 N N N 0 -0.468 -0.773 -1.227
24 H8 H H8 N N N 0 -1.978 -0.208 -1.965
25 H10 H H10 N N N 0 -2.34 2.689 -0.433
26 H11 H H11 N N N 0 -3.067 1.351 -1.34
27 H12 H H12 N N N 0 -3.259 1.964 1.622
28 H13 H H13 N N N 0 -4.567 1.694 0.453
29 H14 H H14 N N N 0 -4.526 -0.298 1.728
30 H15 H H15 N N N 0 -2.756 -0.34 1.784
31 H16 H H16 N N N 0 -0.261 1.793 -1.798
32 H17 H H17 N N N 0 -0.212 2.628 -0.227
33 H18 H H18 N N N 0 1.133 -0.15 -2.216
34 H19 H H19 N N N 0 3.207 -1.347 -1.645
35 H20 H H20 N N N 0 3.323 0.652 2.121
36 H21 H H21 N N N 0 1.252 1.854 1.546
37 H22 H H22 N N N 0 4.716 -1.292 1.703
38 H23 H H23 N N N 0 4.667 -2.127 0.132
39 H24 H H24 N N N 0 6.684 -0.843 0.395
40 H25 H H25 N N N 0 5.761 -0.175 -0.817



5R8 : Chemical Bonds

Total Number of Bonds: 41
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N36 C35 N C sing 1.47 N N
2 C35 C28 C C sing 1.51 N N
3 C28 C27 C C doub 1.38 N Y
4 C28 C29 C C sing 1.38 N Y
5 C27 C26 C C sing 1.38 N Y
6 C29 C30 C C doub 1.38 N Y
7 C26 C23 C C doub 1.38 N Y
8 C30 C23 C C sing 1.38 N Y
9 C23 C22 C C sing 1.51 N N
10 C7 C6 C C sing 1.46 N N
11 C7 N8 C N sing 1.48 N N
12 C6 N2 C N sing 1.48 N N
13 C1 N2 C N sing 1.47 N N
14 C22 N8 C N sing 1.47 N N
15 N8 C9 N C sing 1.44 N N
16 N2 C11 N C sing 1.44 N N
17 C9 C10 C C sing 1.54 N N
18 C11 C10 C C sing 1.54 N N
19 C6 H1 C H sing 1.09 N N
20 C6 H2 C H sing 1.09 N N
21 C1 H3 C H sing 1.09 N N
22 C1 H4 C H sing 1.09 N N
23 C1 H5 C H sing 1.09 N N
24 C7 H7 C H sing 1.09 N N
25 C7 H8 C H sing 1.09 N N
26 C9 H10 C H sing 1.09 N N
27 C9 H11 C H sing 1.09 N N
28 C10 H12 C H sing 1.09 N N
29 C10 H13 C H sing 1.09 N N
30 C11 H14 C H sing 1.09 N N
31 C11 H15 C H sing 1.09 N N
32 C22 H16 C H sing 1.09 N N
33 C22 H17 C H sing 1.09 N N
34 C26 H18 C H sing 1.08 N N
35 C27 H19 C H sing 1.08 N N
36 C29 H20 C H sing 1.08 N N
37 C30 H21 C H sing 1.08 N N
38 C35 H22 C H sing 1.09 N N
39 C35 H23 C H sing 1.09 N N
40 N36 H24 N H sing 1.01 N N
41 N36 H25 N H sing 1.01 N N



5R8 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
5R8 5eqe Open in New Window Bound ligand 2 1