Chemical Components in the PDB

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A3Y : Summary

Code

A3Y

One-letter code

X

Molecule name

6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3S)-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile

Systematic names

ProgramVersionName
ACDLabs 12.01 6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3S)-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile
OpenEye OEToolkits 2.0.6 6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-[(3~{S})-3-(hydroxymethyl)piperidin-1-yl]-4-(trifluoromethyl)pyridine-3-carbonitrile

Formula

C19 H26 F3 N5 O2

Formal charge

0

Molecular weight

413.437 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 N3(CCN(c2cc(C(F)(F)F)c(c(N1CC(CCC1)CO)n2)C#N)CC3)CCO
SMILES CACTVS 3.385 OCCN1CCN(CC1)c2cc(c(C#N)c(n2)N3CCC[CH](CO)C3)C(F)(F)F
SMILES OpenEye OEToolkits 2.0.6 c1c(c(c(nc1N2CCN(CC2)CCO)N3CCCC(C3)CO)C#N)C(F)(F)F
Canonical SMILES CACTVS 3.385 OCCN1CCN(CC1)c2cc(c(C#N)c(n2)N3CCC[C@H](CO)C3)C(F)(F)F
Canonical SMILES OpenEye OEToolkits 2.0.6 c1c(c(c(nc1N2CCN(CC2)CCO)N3CCC[C@@H](C3)CO)C#N)C(F)(F)F

IUPAC InChI

InChI=1S/C19H26F3N5O2/c20-19(21,22)16-10-17(26-6-4-25(5-7-26)8-9-28)24-18(15(16)11-23)27-3-1-2-14(12-27)13-29/h10,14,28-29H,1-9,12-13H2/t14-/m0/s1

IUPAC InChI key

XNJVLRJGPUMHDH-AWEZNQCLSA-N
A3Y

wwPDB Information

Atom count

55 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-07-05

Last modified at

2017-09-08

Status

Released

Obsoleted

Not Assigned



A3Y : 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 N3 N N1 N N N 0 -4.685 0.066 0.014
2 C4 C C1 N Y N 0 1.37 -0.065 -0.358
3 N2 N N2 N N N 0 -2.046 0.942 -0.595
4 C7 C C2 N N N 0 -4.266 1.443 0.307
5 C6 C C3 N N N 0 -2.759 1.468 0.577
6 C9 C C4 N N N 0 -2.466 -0.436 -0.889
7 C13 C C5 N N N 0 2.901 -3.007 -1.966
8 C8 C C6 N N N 0 -3.972 -0.461 -1.158
9 N5 N N3 N N N 0 4.583 1.186 0.235
10 C18 C C7 N N N 0 3.456 1.166 0.1
11 C16 C C8 N N N 0 1.686 -2.215 0.541
12 C19 C C9 N N N 0 1.95 3.632 0.357
13 C1 C C10 N Y N 0 -0.085 2.245 -0.128
14 C2 C C11 N Y N 0 1.282 2.318 0.045
15 C3 C C12 N Y N 0 2.034 1.141 -0.071
16 N1 N N4 N Y N 0 0.057 -0.085 -0.52
17 C5 C C13 N Y N 0 -0.674 1.015 -0.416
18 C10 C C14 N N N 0 -6.14 -0.012 -0.176
19 C11 C C15 N N N 0 -6.601 -1.46 0.004
20 O1 O O1 N N N 0 -6.352 -1.875 1.348
21 N4 N N5 N N N 0 2.095 -1.238 -0.476
22 C12 C C16 N N N 0 1.975 -1.797 -1.829
23 C14 C C17 N N N 0 2.516 -4.059 -0.923
24 C15 C C18 S N N 0 2.604 -3.437 0.474
25 C17 C C19 N N N 0 2.163 -4.464 1.519
26 O2 O O2 N N N 0 3.088 -5.553 1.536
27 F1 F F1 N N N 0 2.873 3.937 -0.648
28 F2 F F2 N N N 0 0.984 4.642 0.424
29 F3 F F3 N N N 0 2.612 3.539 1.586
30 H4 H H2 N N N 0 -4.493 2.082 -0.546
31 H5 H H3 N N N 0 -4.798 1.806 1.186
32 H2 H H4 N N N 0 -2.535 0.851 1.446
33 H3 H H5 N N N 0 -2.441 2.493 0.766
34 H8 H H6 N N N 0 -1.933 -0.799 -1.768
35 H9 H H7 N N N 0 -2.238 -1.075 -0.036
36 H18 H H8 N N N 0 2.8 -3.431 -2.965
37 H17 H H9 N N N 0 3.933 -2.696 -1.806
38 H7 H H10 N N N 0 -4.291 -1.486 -1.348
39 H6 H H11 N N N 0 -4.196 0.157 -2.028
40 H23 H H12 N N N 0 1.757 -1.761 1.529
41 H22 H H13 N N N 0 0.657 -2.522 0.355
42 H1 H H14 N N N 0 -0.693 3.134 -0.045
43 H10 H H15 N N N 0 -6.637 0.622 0.558
44 H11 H H16 N N N 0 -6.394 0.328 -1.181
45 H13 H H17 N N N 0 -7.668 -1.53 -0.206
46 H12 H H18 N N N 0 -6.052 -2.104 -0.683
47 H14 H H19 N N N 0 -6.621 -2.785 1.535
48 H16 H H20 N N N 0 2.255 -1.04 -2.561
49 H15 H H21 N N N 0 0.944 -2.106 -2.003
50 H19 H H22 N N N 0 1.497 -4.399 -1.107
51 H20 H H23 N N N 0 3.2 -4.905 -0.989
52 H21 H H24 N N N 0 3.631 -3.133 0.674
53 H24 H H25 N N N 0 2.137 -3.994 2.502
54 H25 H H26 N N N 0 1.17 -4.836 1.267
55 H26 H H27 N N N 0 2.871 -6.244 2.177



A3Y : 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 C10 C11 C C sing 1.53 N N
2 C10 N3 C N sing 1.47 N N
3 C11 O1 C O sing 1.43 N N
4 C7 N3 C N sing 1.47 N N
5 C7 C6 C C sing 1.53 N N
6 N3 C8 N C sing 1.47 N N
7 C6 N2 C N sing 1.47 N N
8 C8 C9 C C sing 1.53 N N
9 F1 C19 F C sing 1.4 N N
10 F3 C19 F C sing 1.4 N N
11 C1 C5 C C doub 1.39 N Y
12 C1 C2 C C sing 1.38 N Y
13 N2 C5 N C sing 1.39 N N
14 N2 C9 N C sing 1.47 N N
15 C19 C2 C C sing 1.51 N N
16 C19 F2 C F sing 1.4 N N
17 C5 N1 C N sing 1.32 N Y
18 C2 C3 C C doub 1.4 N Y
19 N1 C4 N C doub 1.32 N Y
20 C3 C18 C C sing 1.43 N N
21 C3 C4 C C sing 1.41 N Y
22 C18 N5 C N trip 1.14 N N
23 C4 N4 C N sing 1.38 N N
24 N4 C16 N C sing 1.47 N N
25 N4 C12 N C sing 1.47 N N
26 C16 C15 C C sing 1.53 N N
27 O2 C17 O C sing 1.43 N N
28 C12 C13 C C sing 1.53 N N
29 C15 C17 C C sing 1.53 N N
30 C15 C14 C C sing 1.53 N N
31 C13 C14 C C sing 1.53 N N
32 C7 H4 C H sing 1.09 N N
33 C7 H5 C H sing 1.09 N N
34 C6 H2 C H sing 1.09 N N
35 C6 H3 C H sing 1.09 N N
36 C9 H8 C H sing 1.09 N N
37 C9 H9 C H sing 1.09 N N
38 C13 H18 C H sing 1.09 N N
39 C13 H17 C H sing 1.09 N N
40 C8 H7 C H sing 1.09 N N
41 C8 H6 C H sing 1.09 N N
42 C16 H23 C H sing 1.09 N N
43 C16 H22 C H sing 1.09 N N
44 C1 H1 C H sing 1.08 N N
45 C10 H10 C H sing 1.09 N N
46 C10 H11 C H sing 1.09 N N
47 C11 H13 C H sing 1.09 N N
48 C11 H12 C H sing 1.09 N N
49 O1 H14 O H sing 0.97 N N
50 C12 H16 C H sing 1.09 N N
51 C12 H15 C H sing 1.09 N N
52 C14 H19 C H sing 1.09 N N
53 C14 H20 C H sing 1.09 N N
54 C15 H21 C H sing 1.09 N N
55 C17 H24 C H sing 1.09 N N
56 C17 H25 C H sing 1.09 N N
57 O2 H26 O H sing 0.97 N N



A3Y : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
A3Y 5wbr Open in New Window Bound ligand 2 1