Chemical Components in the PDB

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487 : Summary

Code

487

One-letter code

X

Molecule name

6-[(1S)-1-(azepan-1-yl)ethyl]-N,N-dimethyl-1,3,5-triazine-2,4-diamine

Systematic names

ProgramVersionName
ACDLabs 12.01 6-[(1S)-1-(azepan-1-yl)ethyl]-N,N-dimethyl-1,3,5-triazine-2,4-diamine
OpenEye OEToolkits 1.9.2 6-[(1S)-1-(azepan-1-yl)ethyl]-N2,N2-dimethyl-1,3,5-triazine-2,4-diamine

Formula

C13 H24 N6

Formal charge

0

Molecular weight

264.37 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n1c(nc(nc1C(N2CCCCCC2)C)N(C)C)N
SMILES CACTVS 3.385 C[CH](N1CCCCCC1)c2nc(N)nc(n2)N(C)C
SMILES OpenEye OEToolkits 1.9.2 CC(c1nc(nc(n1)N(C)C)N)N2CCCCCC2
Canonical SMILES CACTVS 3.385 C[C@H](N1CCCCCC1)c2nc(N)nc(n2)N(C)C
Canonical SMILES OpenEye OEToolkits 1.9.2 C[C@@H](c1nc(nc(n1)N(C)C)N)N2CCCCCC2

IUPAC InChI

InChI=1S/C13H24N6/c1-10(19-8-6-4-5-7-9-19)11-15-12(14)17-13(16-11)18(2)3/h10H,4-9H2,1-3H3,(H2,14,15,16,17)/t10-/m0/s1

IUPAC InChI key

VXAHGJQOHMSESG-JTQLQIEISA-N
487

wwPDB Information

Atom count

43 (19 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-02-11

Last modified at

2016-02-26

Status

Released

Obsoleted

Not Assigned



487 : Atoms of Molecule

Total Number of Atoms: 43
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 -2.662 0.159 0.186
2 C5 C C2 N N N 0 -3.772 2.123 1.179
3 C6 C C3 N N N 0 -4.977 -0.102 0.989
4 N1 N N1 N N N 0 -1.589 -2.976 -1.122
5 C7 C C4 N N N 0 3.077 1.219 -0.587
6 C8 C C5 N N N 0 4.354 0.375 -0.38
7 N2 N N2 N Y N 0 -2.668 -1.118 -0.178
8 C9 C C6 N N N 0 4.591 0.198 1.098
9 C10 C C7 N N N 0 3.964 -1.098 1.649
10 C11 C C8 N N N 0 2.565 -1.354 1.063
11 C12 C C9 N N N 0 1.759 -0.082 0.973
12 N3 N N3 N N N 0 -3.781 0.715 0.773
13 N4 N N4 N Y N 0 -1.575 0.901 -0.011
14 C3 C C10 N Y N 0 -1.589 -1.649 -0.743
15 N N N5 N Y N 0 -0.507 -0.9 -0.941
16 C2 C C11 N Y N 0 -0.503 0.37 -0.573
17 C1 C C12 S N N 0 0.724 1.214 -0.799
18 C C C13 N N N 0 0.83 1.572 -2.283
19 N5 N N6 N N N 0 1.918 0.463 -0.39
20 H1 H H1 N N N 0 -2.804 2.564 0.94
21 H2 H H2 N N N 0 -4.557 2.66 0.648
22 H3 H H3 N N N 0 -3.947 2.192 2.253
23 H4 H H4 N N N 0 -4.922 -0.575 1.97
24 H5 H H5 N N N 0 -5.863 0.531 0.941
25 H6 H H6 N N N 0 -5.037 -0.87 0.218
26 H7 H H7 N N N 0 -2.378 -3.522 -0.977
27 H8 H H8 N N N 0 -0.801 -3.363 -1.534
28 H9 H H9 N N N 0 3.083 2.051 0.117
29 H10 H H10 N N N 0 3.075 1.615 -1.603
30 H11 H H11 N N N 0 4.225 -0.601 -0.848
31 H12 H H12 N N N 0 5.206 0.886 -0.828
32 H13 H H13 N N N 0 5.666 0.175 1.282
33 H14 H H14 N N N 0 4.164 1.049 1.628
34 H15 H H15 N N N 0 4.611 -1.939 1.4
35 H16 H H16 N N N 0 3.886 -1.022 2.733
36 H17 H H17 N N N 0 2.669 -1.781 0.066
37 H18 H H18 N N N 0 2.036 -2.063 1.701
38 H19 H H19 N N N 0 0.708 -0.297 1.163
39 H20 H H20 N N N 0 2.126 0.639 1.703
40 H21 H H21 N N N 0 0.65 2.128 -0.209
41 H22 H H22 N N N 0 -0.056 2.13 -2.586
42 H23 H H23 N N N 0 1.717 2.184 -2.447
43 H24 H H24 N N N 0 0.904 0.659 -2.873



487 : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N1 C3 N C sing 1.38 N N
2 C3 N2 C N doub 1.33 N Y
3 C3 N C N sing 1.33 N Y
4 N2 C4 N C sing 1.33 N Y
5 N C2 N C doub 1.32 N Y
6 C C1 C C sing 1.53 N N
7 C5 N3 C N sing 1.47 N N
8 C4 N3 C N sing 1.38 N N
9 C4 N4 C N doub 1.33 N Y
10 C2 N4 C N sing 1.32 N Y
11 C2 C1 C C sing 1.51 N N
12 N3 C6 N C sing 1.46 N N
13 C1 N5 C N sing 1.47 N N
14 C7 N5 C N sing 1.4 N N
15 C7 C8 C C sing 1.54 N N
16 N5 C12 N C sing 1.48 N N
17 C8 C9 C C sing 1.51 N N
18 C12 C11 C C sing 1.51 N N
19 C9 C10 C C sing 1.54 N N
20 C10 C11 C C sing 1.54 N N
21 C5 H1 C H sing 1.09 N N
22 C5 H2 C H sing 1.09 N N
23 C5 H3 C H sing 1.09 N N
24 C6 H4 C H sing 1.09 N N
25 C6 H5 C H sing 1.09 N N
26 C6 H6 C H sing 1.09 N N
27 N1 H7 N H sing 0.97 N N
28 N1 H8 N H sing 0.97 N N
29 C7 H9 C H sing 1.09 N N
30 C7 H10 C H sing 1.09 N N
31 C8 H11 C H sing 1.09 N N
32 C8 H12 C H sing 1.09 N N
33 C9 H13 C H sing 1.09 N N
34 C9 H14 C H sing 1.09 N N
35 C10 H15 C H sing 1.09 N N
36 C10 H16 C H sing 1.09 N N
37 C11 H17 C H sing 1.09 N N
38 C11 H18 C H sing 1.09 N N
39 C12 H19 C H sing 1.09 N N
40 C12 H20 C H sing 1.09 N N
41 C1 H21 C H sing 1.09 N N
42 C H22 C H sing 1.09 N N
43 C H23 C H sing 1.09 N N
44 C H24 C H sing 1.09 N N



487 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
487 4y5n Open in New Window Bound ligand 1 1