Chemical Components in the PDB

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O5X : Summary

Code

O5X

One-letter code

X

Molecule name

6-[4-(dimethylamino)but-1-yn-1-yl]-4-methylpyridin-2-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 6-[4-(dimethylamino)but-1-yn-1-yl]-4-methylpyridin-2-amine
OpenEye OEToolkits 2.0.7 6-[4-(dimethylamino)but-1-ynyl]-4-methyl-pyridin-2-amine

Formula

C12 H17 N3

Formal charge

0

Molecular weight

203.283 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 Cc1cc(C#CCCN(C)C)nc(N)c1
SMILES CACTVS 3.385 CN(C)CCC#Cc1cc(C)cc(N)n1
SMILES OpenEye OEToolkits 2.0.7 Cc1cc(nc(c1)N)C#CCCN(C)C
Canonical SMILES CACTVS 3.385 CN(C)CCC#Cc1cc(C)cc(N)n1
Canonical SMILES OpenEye OEToolkits 2.0.7 Cc1cc(nc(c1)N)C#CCCN(C)C

IUPAC InChI

InChI=1S/C12H17N3/c1-10-8-11(14-12(13)9-10)6-4-5-7-15(2)3/h8-9H,5,7H2,1-3H3,(H2,13,14)

IUPAC InChI key

SWAXYJVGMJZMLB-UHFFFAOYSA-N
O5X

wwPDB Information

Atom count

32 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-04-25

Last modified at

2022-07-08

Status

Released

Obsoleted

Not Assigned



O5X : Atoms of Molecule

Total Number of Atoms: 32
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C02 C C1 N Y N 0 -3.466 -1.053 0.142
2 C03 C C2 N Y N 0 -4.05 0.21 0.19
3 C04 C C3 N Y N 0 -3.252 1.332 0.046
4 C05 C C4 N Y N 0 -1.89 1.159 -0.141
5 C06 C C5 N Y N 0 -1.368 -0.133 -0.179
6 C07 C C6 N N N 0 -3.852 2.714 0.092
7 C08 C C7 N N N 0 0.038 -0.324 -0.372
8 C09 C C8 N N N 0 1.191 -0.481 -0.53
9 C10 C C9 N N N 0 2.636 -0.678 -0.728
10 C11 C C10 N N N 0 3.404 0.002 0.407
11 C13 C C11 N N N 0 5.312 0.504 -0.995
12 C14 C C12 N N N 0 5.603 0.235 1.393
13 N01 N N1 N Y N 0 -2.162 -1.188 -0.033
14 N02 N N2 N N N 0 -4.262 -2.183 0.285
15 N12 N N3 N N N 0 4.846 -0.194 0.21
16 H1 H H1 N N N 0 -5.115 0.314 0.337
17 H2 H H2 N N N 0 -1.241 2.014 -0.257
18 H3 H H3 N N N 0 -3.854 3.075 1.121
19 H4 H H4 N N N 0 -3.262 3.388 -0.529
20 H5 H H5 N N N 0 -4.875 2.678 -0.282
21 H6 H H6 N N N 0 2.861 -1.745 -0.73
22 H7 H H7 N N N 0 2.935 -0.242 -1.681
23 H8 H H8 N N N 0 3.179 1.069 0.41
24 H9 H H9 N N N 0 3.105 -0.434 1.361
25 H10 H H10 N N N 0 5.115 1.572 -0.895
26 H11 H H11 N N N 0 6.383 0.343 -1.118
27 H12 H H12 N N N 0 4.784 0.118 -1.867
28 H13 H H13 N N N 0 5.286 -0.348 2.258
29 H14 H H14 N N N 0 6.668 0.078 1.22
30 H15 H H15 N N N 0 5.417 1.292 1.58
31 H16 H H16 N N N 0 -3.86 -3.066 0.257
32 H17 H H17 N N N 0 -5.219 -2.09 0.414



O5X : Chemical Bonds

Total Number of Bonds: 32
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C07 C04 C C sing 1.51 N N
2 C04 C03 C C doub 1.38 N Y
3 C04 C05 C C sing 1.39 N Y
4 C03 C02 C C sing 1.39 N Y
5 C05 C06 C C doub 1.39 N Y
6 C02 N02 C N sing 1.39 N N
7 C02 N01 C N doub 1.32 N Y
8 C06 N01 C N sing 1.33 N Y
9 C06 C08 C C sing 1.43 N N
10 C08 C09 C C trip 1.17 N N
11 C14 N12 C N sing 1.47 N N
12 C11 C10 C C sing 1.53 N N
13 C11 N12 C N sing 1.47 N N
14 C09 C10 C C sing 1.47 N N
15 N12 C13 N C sing 1.47 N N
16 C03 H1 C H sing 1.08 N N
17 C05 H2 C H sing 1.08 N N
18 C07 H3 C H sing 1.09 N N
19 C07 H4 C H sing 1.09 N N
20 C07 H5 C H sing 1.09 N N
21 C10 H6 C H sing 1.09 N N
22 C10 H7 C H sing 1.09 N N
23 C11 H8 C H sing 1.09 N N
24 C11 H9 C H sing 1.09 N N
25 C13 H10 C H sing 1.09 N N
26 C13 H11 C H sing 1.09 N N
27 C13 H12 C H sing 1.09 N N
28 C14 H13 C H sing 1.09 N N
29 C14 H14 C H sing 1.09 N N
30 C14 H15 C H sing 1.09 N N
31 N02 H16 N H sing 0.97 N N
32 N02 H17 N H sing 0.97 N N



O5X : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
O5X 7us7 Open in New Window Bound ligand 4 1