Chemical Components in the PDB

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SVJ : Summary

Code

SVJ

One-letter code

X

Molecule name

(1~{S},5~{R})-8-methyl-8-azabicyclo[3.2.1]octan-3-amine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (1~{S},5~{R})-8-methyl-8-azabicyclo[3.2.1]octan-3-amine

Formula

C8 H16 N2

Formal charge

0

Molecular weight

140.226 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1[CH]2CC[CH]1C[CH](N)C2
SMILES OpenEye OEToolkits 2.0.6 CN1C2CCC1CC(C2)N
Canonical SMILES CACTVS 3.385 CN1[C@H]2CC[C@@H]1C[C@H](N)C2
Canonical SMILES OpenEye OEToolkits 2.0.6 CN1[C@@H]2CC[C@H]1CC(C2)N

IUPAC InChI

InChI=1S/C8H16N2/c1-10-7-2-3-8(10)5-6(9)4-7/h6-8H,2-5,9H2,1H3/t6-,7+,8-

IUPAC InChI key

HJGMRAKQWLKWMH-RNLVFQAGSA-N
SVJ

wwPDB Information

Atom count

26 (10 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-03-11

Last modified at

2020-07-17

Status

Released

Obsoleted

Not Assigned



SVJ : Atoms of Molecule

Total Number of Atoms: 26
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N N N 0 -2.049 -0.001 0.733
2 C4 C C1 R N N 0 0.533 1.163 -0.112
3 C5 C C2 N N N 0 -0.768 1.268 -0.924
4 C6 C C3 R N N 0 -1.613 0.017 -0.669
5 C7 C C4 N N N 0 -0.784 -1.236 -0.962
6 C2 C C7 N N N 0 0.149 -0.795 1.306
7 N N N2 N N N 0 1.304 0.005 -0.638
8 C C C5 N N N 0 2.676 0.004 -0.112
9 C1 C C6 S N N 0 0.518 -1.172 -0.148
10 C3 C C8 N N N 0 0.159 0.747 1.329
11 H1 H H1 N N N 0 -2.576 0.829 0.96
12 H2 H H2 N N N 0 -2.582 -0.834 0.936
13 H4 H H4 N N N 0 1.109 2.088 -0.138
14 H5 H H5 N N N 0 -1.322 2.153 -0.612
15 H6 H H6 N N N 0 -0.531 1.341 -1.985
16 H7 H H7 N N N 0 -2.488 0.032 -1.32
17 H8 H H8 N N N 0 -1.349 -2.124 -0.677
18 H9 H H9 N N N 0 -0.548 -1.277 -2.025
19 H11 H H11 N N N 0 2.648 -0.06 0.975
20 H12 H H12 N N N 0 3.218 -0.854 -0.513
21 H13 H H13 N N N 0 3.18 0.923 -0.41
22 H14 H H14 N N N 0 1.088 -2.099 -0.211
23 H15 H H15 N N N 0 -0.843 -1.172 1.555
24 H16 H H16 N N N 0 0.891 -1.19 2.0
25 H18 H H18 N N N 0 -0.833 1.12 1.586
26 H17 H H17 N N N 0 0.9 1.121 2.036



SVJ : Chemical Bonds

Total Number of Bonds: 27
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C7 C1 C C sing 1.54 N N
2 C7 C6 C C sing 1.53 N N
3 C1 N C N sing 1.5 N N
4 C1 C2 C C sing 1.55 N N
5 C6 N1 C N sing 1.47 N N
6 C6 C5 C C sing 1.53 N N
7 N C N C sing 1.47 N N
8 N C4 N C sing 1.49 N N
9 C2 C3 C C sing 1.54 N N
10 C5 C4 C C sing 1.54 N N
11 C4 C3 C C sing 1.55 N N
12 N1 H1 N H sing 1.01 N N
13 N1 H2 N H sing 1.01 N N
14 C4 H4 C H sing 1.09 N N
15 C5 H5 C H sing 1.09 N N
16 C5 H6 C H sing 1.09 N N
17 C6 H7 C H sing 1.09 N N
18 C7 H8 C H sing 1.09 N N
19 C7 H9 C H sing 1.09 N N
20 C H11 C H sing 1.09 N N
21 C H12 C H sing 1.09 N N
22 C H13 C H sing 1.09 N N
23 C1 H14 C H sing 1.09 N N
24 C2 H15 C H sing 1.09 N N
25 C2 H16 C H sing 1.09 N N
26 C3 H17 C H sing 1.09 N N
27 C3 H18 C H sing 1.09 N N



SVJ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
SVJ 5ra5 Open in New Window Bound ligand 1 1