Chemical Components in the PDB

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IUY : Summary

Code

IUY

One-letter code

X

Molecule name

ethyl (5R)-5-(4-cyanophenyl)-7-methyl-8-[3-(trifluoromethyl)phenyl]-1,5-dihydroimidazo[1,2-a]pyrimidin-4-ium-6-carboxylate

Systematic names

ProgramVersionName
OpenEye OEToolkits 1.7.6 ethyl (5R)-5-(4-cyanophenyl)-7-methyl-8-[3-(trifluoromethyl)phenyl]-1,5-dihydroimidazo[1,2-a]pyrimidin-4-ium-6-carboxylate

Formula

C24 H20 F3 N4 O2

Formal charge

1

Molecular weight

453.436 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCOC(=O)C1=C(C)N(c2cccc(c2)C(F)(F)F)c3[nH]cc[n+]3[CH]1c4ccc(cc4)C#N
SMILES OpenEye OEToolkits 1.7.6 CCOC(=O)C1=C(N(c2[nH]cc[n+]2C1c3ccc(cc3)C#N)c4cccc(c4)C(F)(F)F)C
Canonical SMILES CACTVS 3.385 CCOC(=O)C1=C(C)N(c2cccc(c2)C(F)(F)F)c3[nH]cc[n+]3[C@@H]1c4ccc(cc4)C#N
Canonical SMILES OpenEye OEToolkits 1.7.6 CCOC(=O)C1=C(N(c2[nH]cc[n+]2[C@@H]1c3ccc(cc3)C#N)c4cccc(c4)C(F)(F)F)C

IUPAC InChI

InChI=1S/C24H19F3N4O2/c1-3-33-22(32)20-15(2)31(19-6-4-5-18(13-19)24(25,26)27)23-29-11-12-30(23)21(20)17-9-7-16(14-28)8-10-17/h4-13,21H,3H2,1-2H3/p+1/t21-/m1/s1

IUPAC InChI key

JHIVXCHUXFMPOR-OAQYLSRUSA-O
IUY

wwPDB Information

Atom count

53 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2015-09-24

Last modified at

2016-07-29

Status

Released

Obsoleted

Not Assigned



IUY : Atoms of Molecule

Total Number of Atoms: 53
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 -1.16 1.507 -0.328
2 C2 C C2 R N N 0 -1.897 1.081 0.911
3 C3 C C3 N N N 0 0.181 1.53 -0.405
4 N4 N N4 N N N 0 0.966 1.172 0.664
5 C5 C C5 N N N 0 0.839 1.958 -1.692
6 C6 C C6 N Y N 0 -2.513 -0.276 0.687
7 C7 C C7 N Y N 0 -3.884 -0.434 0.782
8 C8 C C8 N Y N 0 -4.455 -1.674 0.577
9 C9 C C9 N Y N 0 -3.645 -2.77 0.273
10 C10 C C10 N Y N 0 -2.262 -2.603 0.179
11 C11 C C11 N Y N 0 -1.705 -1.357 0.381
12 C12 C C12 N N N 0 -1.91 1.894 -1.462
13 O13 O O13 N N N 0 -1.342 2.324 -2.449
14 O14 O O14 N N N 0 -3.255 1.787 -1.449
15 C15 C C15 N N N 0 -3.949 2.197 -2.63
16 C16 C C16 N N N 0 -5.454 2.004 -2.429
17 C17 C C17 N N N 0 -4.23 -4.059 0.06
18 N18 N N18 N N N 0 -4.694 -5.082 -0.109
19 N19 N N19 N Y N 1 -0.966 1.013 2.042
20 C20 C C20 N Y N 0 0.345 1.053 1.904
21 N21 N N21 N Y N 0 0.914 0.962 3.127
22 C22 C C22 N Y N 0 -0.113 0.869 4.04
23 C23 C C23 N Y N 0 -1.265 0.903 3.342
24 C24 C C24 N Y N 0 2.336 0.936 0.512
25 C25 C C25 N Y N 0 3.259 1.804 1.082
26 C26 C C26 N Y N 0 4.612 1.568 0.93
27 C27 C C27 N Y N 0 5.047 0.47 0.211
28 C28 C C28 N Y N 0 4.131 -0.396 -0.357
29 C29 C C29 N Y N 0 2.777 -0.169 -0.204
30 C30 C C30 N N N 0 4.61 -1.591 -1.14
31 F31 F F31 N N N 0 6.009 -1.611 -1.151
32 F32 F F32 N N N 0 4.131 -2.762 -0.543
33 F33 F F33 N N N 0 4.135 -1.51 -2.453
34 H2 H H2 N N N 0 -2.683 1.803 1.133
35 H5 H H5 N N N 0 0.567 2.99 -1.914
36 H5A H H5A N N N 0 1.921 1.881 -1.59
37 H5B H H5B N N N 0 0.504 1.311 -2.503
38 H7 H H7 N N N 0 -4.51 0.414 1.017
39 H8 H H8 N N N 0 -5.525 -1.796 0.652
40 H10 H H10 N N N 0 -1.629 -3.447 -0.055
41 H11 H H11 N N N 0 -0.636 -1.226 0.305
42 H15 H H15 N N N 0 -3.741 3.248 -2.827
43 H15A H H15A N N N 0 -3.615 1.595 -3.475
44 H16 H H16 N N N 0 -5.662 0.952 -2.232
45 H16A H H16A N N N 0 -5.788 2.605 -1.584
46 H16B H H16B N N N 0 -5.983 2.316 -3.329
47 HN21 H HN21 N N N 0 1.863 0.962 3.325
48 H22 H H22 N N N 0 -0.014 0.785 5.112
49 H23 H H23 N N N 0 -2.259 0.851 3.76
50 H25 H H25 N N N 0 2.92 2.662 1.643
51 H26 H H26 N N N 0 5.33 2.242 1.373
52 H27 H H27 N N N 0 6.105 0.288 0.093
53 H29 H H29 N N N 0 2.062 -0.848 -0.645



IUY : Chemical Bonds

Total Number of Bonds: 56
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.5 N N
2 C1 C3 C C doub 1.34 N N
3 C1 C12 C C sing 1.41 N N
4 C2 C6 C C sing 1.51 N N
5 C2 N19 C N sing 1.47 N N
6 C3 N4 C N sing 1.37 N N
7 C3 C5 C C sing 1.51 N N
8 N4 C20 N C sing 1.39 N N
9 N4 C24 N C sing 1.4 N N
10 C6 C7 C C doub 1.38 N Y
11 C6 C11 C C sing 1.38 N Y
12 C7 C8 C C sing 1.38 N Y
13 C8 C9 C C doub 1.4 N Y
14 C9 C10 C C sing 1.4 N Y
15 C9 C17 C C sing 1.43 N N
16 C10 C11 C C doub 1.38 N Y
17 C12 O13 C O doub 1.22 N N
18 C12 O14 C O sing 1.35 N N
19 O14 C15 O C sing 1.43 N N
20 C15 C16 C C sing 1.53 N N
21 C17 N18 C N trip 1.14 N N
22 N19 C20 N C doub 1.32 N Y
23 N19 C23 N C sing 1.34 N Y
24 C20 N21 C N sing 1.35 N Y
25 N21 C22 N C sing 1.38 N Y
26 C22 C23 C C doub 1.35 N Y
27 C24 C25 C C doub 1.39 N Y
28 C24 C29 C C sing 1.39 N Y
29 C25 C26 C C sing 1.38 N Y
30 C26 C27 C C doub 1.38 N Y
31 C27 C28 C C sing 1.38 N Y
32 C28 C29 C C doub 1.38 N Y
33 C28 C30 C C sing 1.51 N N
34 C30 F31 C F sing 1.4 N N
35 C30 F32 C F sing 1.4 N N
36 C30 F33 C F sing 1.4 N N
37 C2 H2 C H sing 1.09 N N
38 C5 H5 C H sing 1.09 N N
39 C5 H5A C H sing 1.09 N N
40 C5 H5B C H sing 1.09 N N
41 C7 H7 C H sing 1.08 N N
42 C8 H8 C H sing 1.08 N N
43 C10 H10 C H sing 1.08 N N
44 C11 H11 C H sing 1.08 N N
45 C15 H15 C H sing 1.09 N N
46 C15 H15A C H sing 1.09 N N
47 C16 H16 C H sing 1.09 N N
48 C16 H16A C H sing 1.09 N N
49 C16 H16B C H sing 1.09 N N
50 N21 HN21 N H sing 0.97 N N
51 C22 H22 C H sing 1.08 N N
52 C23 H23 C H sing 1.08 N N
53 C25 H25 C H sing 1.08 N N
54 C26 H26 C H sing 1.08 N N
55 C27 H27 C H sing 1.08 N N
56 C29 H29 C H sing 1.08 N N



IUY : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
IUY 5a8x Open in New Window Bound ligand 1 1