Chemical Components in the PDB

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VYG : Summary

Code

VYG

One-letter code

X

Molecule name

6-ethyl-5-[3-({3-[4-(trifluoromethyl)piperidin-1-yl]pyridin-2-yl}oxy)propoxy]pyrimidine-2,4-diamine

Systematic names

ProgramVersionName
ACDLabs 12.01 6-ethyl-5-[3-({3-[4-(trifluoromethyl)piperidin-1-yl]pyridin-2-yl}oxy)propoxy]pyrimidine-2,4-diamine
OpenEye OEToolkits 2.0.7 6-ethyl-5-[3-[3-[4-(trifluoromethyl)piperidin-1-yl]pyridin-2-yl]oxypropoxy]pyrimidine-2,4-diamine

Formula

C20 H27 F3 N6 O2

Formal charge

0

Molecular weight

440.463 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C(C)c1c(c(nc(n1)N)N)OCCCOc2c(cccn2)N3CCC(C(F)(F)F)CC3
SMILES CACTVS 3.385 CCc1nc(N)nc(N)c1OCCCOc2ncccc2N3CCC(CC3)C(F)(F)F
SMILES OpenEye OEToolkits 2.0.7 CCc1c(c(nc(n1)N)N)OCCCOc2c(cccn2)N3CCC(CC3)C(F)(F)F
Canonical SMILES CACTVS 3.385 CCc1nc(N)nc(N)c1OCCCOc2ncccc2N3CCC(CC3)C(F)(F)F
Canonical SMILES OpenEye OEToolkits 2.0.7 CCc1c(c(nc(n1)N)N)OCCCOc2c(cccn2)N3CCC(CC3)C(F)(F)F

IUPAC InChI

InChI=1S/C20H27F3N6O2/c1-2-14-16(17(24)28-19(25)27-14)30-11-4-12-31-18-15(5-3-8-26-18)29-9-6-13(7-10-29)20(21,22)23/h3,5,8,13H,2,4,6-7,9-12H2,1H3,(H4,24,25,27,28)

IUPAC InChI key

KHPDUBAKUFVHPS-UHFFFAOYSA-N
VYG

wwPDB Information

Atom count

58 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-09-21

Last modified at

2021-03-12

Status

Released

Obsoleted

Not Assigned



VYG : Atoms of Molecule

Total Number of Atoms: 58
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N N N 0 -5.147 0.917 2.286
2 C2 C C2 N Y N 0 -5.791 0.739 0.935
3 C3 C C3 N Y N 0 -7.687 0.503 -0.356
4 C4 C C4 N Y N 0 -5.652 0.486 -1.439
5 C5 C C5 N Y N 0 -5.011 0.651 -0.205
6 C6 C C6 N N N 0 -2.942 -0.512 -0.039
7 C7 C C7 N N N 0 -1.437 -0.235 -0.043
8 N1 N N1 N N N 0 -9.069 0.424 -0.426
9 C8 C C8 N N N 0 -0.675 -1.559 0.053
10 C9 C C9 N Y N 0 1.555 -2.376 0.13
11 C10 C C10 N Y N 0 1.806 -4.665 0.275
12 C11 C C11 N Y N 0 3.183 -4.557 0.281
13 N2 N N2 N Y N 0 -6.979 0.42 -1.472
14 C12 C C12 N Y N 0 3.767 -3.301 0.207
15 C13 C C13 N Y N 0 2.937 -2.189 0.13
16 C14 C C14 N N N 0 4.245 -0.726 -1.188
17 C15 C C15 N N N 0 4.7 0.731 -1.307
18 C16 C C16 N N N 0 5.566 1.091 -0.096
19 C17 C C17 N N N 0 5.974 2.563 -0.179
20 C18 C C18 N N N 0 4.762 0.853 1.185
21 C19 C C19 N N N 0 4.306 -0.607 1.232
22 O1 O O1 N N N 0 0.73 -1.3 0.049
23 N3 N N3 N N N 0 -4.913 0.393 -2.61
24 N N N4 N Y N 0 -7.11 0.659 0.825
25 C C C20 N N N 0 -5.063 2.408 2.618
26 O O O2 N N N 0 -3.654 0.724 -0.129
27 F F F1 N N N 0 6.765 2.89 0.927
28 F1 F F2 N N N 0 6.703 2.779 -1.354
29 F2 F F3 N N N 0 4.828 3.365 -0.187
30 N4 N N5 N Y N 0 1.041 -3.591 0.201
31 N5 N N6 N N N 0 3.48 -0.901 0.054
32 H1 H H1 N N N 0 -5.745 0.409 3.043
33 H2 H H2 N N N 0 -4.144 0.491 2.27
34 H3 H H3 N N N 0 -3.198 -1.142 -0.891
35 H4 H H4 N N N 0 -3.215 -1.022 0.885
36 H5 H H5 N N N 0 -1.164 0.274 -0.967
37 H6 H H6 N N N 0 -1.181 0.394 0.808
38 H7 H H7 N N N 0 -9.6 0.484 0.384
39 H8 H H8 N N N 0 -9.505 0.31 -1.285
40 H9 H H9 N N N 0 -0.948 -2.069 0.977
41 H10 H H10 N N N 0 -0.932 -2.189 -0.799
42 H11 H H11 N N N 0 1.349 -5.641 0.333
43 H12 H H12 N N N 0 3.799 -5.442 0.343
44 H13 H H13 N N N 0 4.841 -3.19 0.209
45 H14 H H14 N N N 0 3.617 -0.981 -2.041
46 H15 H H15 N N N 0 5.118 -1.378 -1.172
47 H16 H H16 N N N 0 5.281 0.857 -2.22
48 H17 H H17 N N N 0 3.827 1.383 -1.337
49 H18 H H18 N N N 0 6.458 0.465 -0.088
50 H19 H H19 N N N 0 5.387 1.066 2.052
51 H20 H H20 N N N 0 3.89 1.507 1.195
52 H21 H H21 N N N 0 5.178 -1.26 1.236
53 H22 H H22 N N N 0 3.721 -0.776 2.136
54 H23 H H23 N N N 0 -3.945 0.441 -2.578
55 H24 H H24 N N N 0 -5.365 0.278 -3.461
56 H25 H H25 N N N 0 -6.059 2.848 2.572
57 H26 H H26 N N N 0 -4.656 2.534 3.622
58 H27 H H27 N N N 0 -4.413 2.905 1.898



VYG : Chemical Bonds

Total Number of Bonds: 60
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N3 C4 N C sing 1.39 N N
2 N2 C4 N C doub 1.33 N Y
3 N2 C3 N C sing 1.32 N Y
4 C4 C5 C C sing 1.4 N Y
5 N1 C3 N C sing 1.39 N N
6 C3 N C N doub 1.32 N Y
7 C6 C7 C C sing 1.53 N N
8 C6 O C O sing 1.43 N N
9 C5 O C O sing 1.36 N N
10 C5 C2 C C doub 1.38 N Y
11 C7 C8 C C sing 1.53 N N
12 F1 C17 F C sing 1.4 N N
13 N C2 N C sing 1.33 N Y
14 F C17 F C sing 1.4 N N
15 C2 C1 C C sing 1.51 N N
16 C17 F2 C F sing 1.4 N N
17 C17 C16 C C sing 1.53 N N
18 C8 O1 C O sing 1.43 N N
19 C18 C16 C C sing 1.53 N N
20 C18 C19 C C sing 1.53 N N
21 C1 C C C sing 1.53 N N
22 O1 C9 O C sing 1.36 N N
23 C16 C15 C C sing 1.53 N N
24 C19 N5 C N sing 1.47 N N
25 C15 C14 C C sing 1.53 N N
26 N5 C14 N C sing 1.47 N N
27 N5 C13 N C sing 1.4 N N
28 C9 C13 C C doub 1.39 N Y
29 C9 N4 C N sing 1.32 N Y
30 C13 C12 C C sing 1.39 N Y
31 N4 C10 N C doub 1.32 N Y
32 C12 C11 C C doub 1.39 N Y
33 C10 C11 C C sing 1.38 N Y
34 C1 H1 C H sing 1.09 N N
35 C1 H2 C H sing 1.09 N N
36 C6 H3 C H sing 1.09 N N
37 C6 H4 C H sing 1.09 N N
38 C7 H5 C H sing 1.09 N N
39 C7 H6 C H sing 1.09 N N
40 N1 H7 N H sing 0.97 N N
41 N1 H8 N H sing 0.97 N N
42 C8 H9 C H sing 1.09 N N
43 C8 H10 C H sing 1.09 N N
44 C10 H11 C H sing 1.08 N N
45 C11 H12 C H sing 1.08 N N
46 C12 H13 C H sing 1.08 N N
47 C14 H14 C H sing 1.09 N N
48 C14 H15 C H sing 1.09 N N
49 C15 H16 C H sing 1.09 N N
50 C15 H17 C H sing 1.09 N N
51 C16 H18 C H sing 1.09 N N
52 C18 H19 C H sing 1.09 N N
53 C18 H20 C H sing 1.09 N N
54 C19 H21 C H sing 1.09 N N
55 C19 H22 C H sing 1.09 N N
56 N3 H23 N H sing 0.97 N N
57 N3 H24 N H sing 0.97 N N
58 C H25 C H sing 1.09 N N
59 C H26 C H sing 1.09 N N
60 C H27 C H sing 1.09 N N



VYG : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
VYG 7k6a Open in New Window Bound ligand 1 1