Chemical Components in the PDB

pdbe.org/chem
spacer

0SB : Summary

Code

0SB

One-letter code

X

Molecule name

N-{6-[3-(piperazin-1-yl)phenyl]pyridin-2-yl}-4-(trifluoromethyl)pyridin-2-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 N-{6-[3-(piperazin-1-yl)phenyl]pyridin-2-yl}-4-(trifluoromethyl)pyridin-2-amine
OpenEye OEToolkits 1.7.6 6-(3-piperazin-1-ylphenyl)-N-[4-(trifluoromethyl)pyridin-2-yl]pyridin-2-amine

Formula

C21 H20 F3 N5

Formal charge

0

Molecular weight

399.412 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 FC(F)(F)c1cc(ncc1)Nc2nc(ccc2)c3cc(ccc3)N4CCNCC4
SMILES CACTVS 3.370 FC(F)(F)c1ccnc(Nc2cccc(n2)c3cccc(c3)N4CCNCC4)c1
SMILES OpenEye OEToolkits 1.7.6 c1cc(cc(c1)N2CCNCC2)c3cccc(n3)Nc4cc(ccn4)C(F)(F)F
Canonical SMILES CACTVS 3.370 FC(F)(F)c1ccnc(Nc2cccc(n2)c3cccc(c3)N4CCNCC4)c1
Canonical SMILES OpenEye OEToolkits 1.7.6 c1cc(cc(c1)N2CCNCC2)c3cccc(n3)Nc4cc(ccn4)C(F)(F)F

IUPAC InChI

InChI=1S/C21H20F3N5/c22-21(23,24)16-7-8-26-20(14-16)28-19-6-2-5-18(27-19)15-3-1-4-17(13-15)29-11-9-25-10-12-29/h1-8,13-14,25H,9-12H2,(H,26,27,28)

IUPAC InChI key

FCPDILGNMHIWJE-UHFFFAOYSA-N
0SB

wwPDB Information

Atom count

49 (29 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2012-05-21

Last modified at

2012-12-07

Status

Released

Obsoleted

Not Assigned



0SB : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 -3.463 -0.414 0.207
2 C2 C C2 N Y N 0 -2.381 0.451 0.154
3 C3 C C3 N Y N 0 -4.758 0.086 0.129
4 C4 C C4 N Y N 0 -2.597 1.822 0.029
5 C5 C C5 N Y N 0 -4.97 1.446 0.0050
6 C6 C C6 N Y N 0 -3.899 2.315 -0.042
7 C7 C C7 N Y N 0 -1.444 2.754 -0.028
8 C11 C C11 N Y N 0 -0.586 4.984 -0.205
9 C12 C C12 N Y N 0 0.69 4.451 -0.13
10 N13 N N13 N N N 0 2.125 2.53 0.064
11 C15 C C15 N Y N 0 3.577 0.611 0.039
12 C17 C C17 N Y N 0 3.73 -0.764 0.058
13 C18 C C18 N Y N 0 1.35 -0.956 0.148
14 C19 C C19 N Y N 0 2.592 -1.557 0.113
15 C27 C C27 N N N 0 -2.122 -3.782 -0.533
16 F23 F F23 N N N 0 5.576 -1.555 1.324
17 C20 C C20 N N N 0 5.102 -1.386 0.018
18 F21 F F21 N N N 0 5.032 -2.63 -0.617
19 F22 F F22 N N N 0 5.974 -0.55 -0.688
20 N16 N N16 N Y N 0 1.233 0.358 0.124
21 C14 C C14 N Y N 0 2.294 1.148 0.076
22 C10 C C10 N Y N 0 0.846 3.073 -0.012
23 N8 N N8 N Y N 0 -0.208 2.275 0.036
24 C9 C C9 N Y N 0 -1.669 4.121 -0.152
25 N24 N N24 N N N 0 -3.252 -1.79 0.332
26 C26 C C26 N N N 0 -4.528 -2.517 0.369
27 C28 C C28 N N N 0 -4.257 -4.008 0.586
28 N29 N N29 N N N 0 -3.398 -4.51 -0.497
29 C25 C C25 N N N 0 -2.394 -2.291 -0.75
30 H1 H H1 N N N 0 -1.375 0.065 0.21
31 H2 H H2 N N N 0 -5.599 -0.59 0.166
32 H3 H H3 N N N 0 -5.978 1.829 -0.055
33 H4 H H4 N N N 0 -4.069 3.377 -0.139
34 H5 H H5 N N N 0 -0.733 6.05 -0.297
35 H6 H H6 N N N 0 1.554 5.097 -0.164
36 H7 H H7 N N N 0 2.898 3.113 0.108
37 H8 H H8 N N N 0 4.44 1.258 0.0010
38 H9 H H9 N N N 0 0.462 -1.57 0.186
39 H10 H H10 N N N 0 2.678 -2.634 0.128
40 H11 H H11 N N N 0 -1.597 -3.922 0.411
41 H12 H H12 N N N 0 -1.51 -4.163 -1.35
42 H13 H H13 N N N 0 -2.677 4.506 -0.208
43 H14 H H14 N N N 0 -5.141 -2.136 1.186
44 H15 H H15 N N N 0 -5.054 -2.377 -0.576
45 H16 H H16 N N N 0 -3.755 -4.15 1.543
46 H17 H H17 N N N 0 -5.2 -4.553 0.585
47 H18 H H18 N N N 0 -3.871 -4.456 -1.387
48 H20 H H20 N N N 0 -1.45 -1.746 -0.749
49 H21 H H21 N N N 0 -2.895 -2.149 -1.708



0SB : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C5 C3 C C doub 1.3819985 N Y
2 C5 C6 C C sing 1.3800039 N Y
3 C3 C1 C C sing 1.3903629 N Y
4 C25 N24 C N sing 1.4689755 N N
5 C25 C27 C C sing 1.5310631 N N
6 C6 C4 C C doub 1.3940208 N Y
7 F22 C20 F C sing 1.399184 N N
8 C1 N24 C N sing 1.3976845 N N
9 C1 C2 C C doub 1.3862748 N Y
10 F21 C20 F C sing 1.3984495 N N
11 N24 C26 N C sing 1.4690385 N N
12 C26 C28 C C sing 1.5308857 N N
13 C27 N29 C N sing 1.4695088 N N
14 C4 C2 C C sing 1.3935286 N Y
15 C4 C7 C C sing 1.4836718 N N
16 C20 F23 C F sing 1.3995974 N N
17 C20 C17 C C sing 1.5069399 N N
18 N29 C28 N C sing 1.4706373 N N
19 C7 C9 C C doub 1.3909314 N Y
20 C7 N8 C N sing 1.3271146 N Y
21 C17 C15 C C doub 1.3836167 N Y
22 C17 C19 C C sing 1.3881347 N Y
23 C9 C11 C C sing 1.3858092 N Y
24 C15 C14 C C sing 1.39134 N Y
25 N8 C10 N C doub 1.3228847 N Y
26 C19 C18 C C doub 1.3802137 N Y
27 C11 C12 C C doub 1.3848791 N Y
28 C10 C12 C C sing 1.3918132 N Y
29 C10 N13 C N sing 1.3915696 N N
30 C14 N13 C N sing 1.3923466 N N
31 C14 N16 C N doub 1.3236786 N Y
32 C18 N16 C N sing 1.3194169 N Y
33 C2 H1 C H sing 1.0789661 N N
34 C3 H2 C H sing 1.0796416 N N
35 C5 H3 C H sing 1.0799782 N N
36 C6 H4 C H sing 1.0798856 N N
37 C11 H5 C H sing 1.0800134 N N
38 C12 H6 C H sing 1.0793369 N N
39 N13 H7 N H sing 0.96920276 N N
40 C15 H8 C H sing 1.0792692 N N
41 C18 H9 C H sing 1.0802703 N N
42 C19 H10 C H sing 1.0805323 N N
43 C27 H11 C H sing 1.089202 N N
44 C27 H12 C H sing 1.0895844 N N
45 C9 H13 C H sing 1.0804744 N N
46 C26 H14 C H sing 1.0901463 N N
47 C26 H15 C H sing 1.0905508 N N
48 C28 H16 C H sing 1.0899619 N N
49 C28 H17 C H sing 1.0891625 N N
50 N29 H18 N H sing 1.009329 N N
51 C25 H20 C H sing 1.0900284 N N
52 C25 H21 C H sing 1.0903802 N N



0SB : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
0SB 4f4p Open in New Window Bound ligand 1 1