Chemical Components in the PDB

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EBE : Summary

Code

EBE

One-letter code

X

Molecule name

(2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (2~{S})-2-(2-fluorophenyl)-2-[4-(2-methylpyrimidin-5-yl)phenyl]-~{N}-oxidanyl-ethanamide

Formula

C19 H16 F N3 O2

Formal charge

0

Molecular weight

337.348 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Cc1ncc(cn1)c2ccc(cc2)[CH](C(=O)NO)c3ccccc3F
SMILES OpenEye OEToolkits 2.0.6 Cc1ncc(cn1)c2ccc(cc2)C(c3ccccc3F)C(=O)NO
Canonical SMILES CACTVS 3.385 Cc1ncc(cn1)c2ccc(cc2)[C@H](C(=O)NO)c3ccccc3F
Canonical SMILES OpenEye OEToolkits 2.0.6 Cc1ncc(cn1)c2ccc(cc2)[C@@H](c3ccccc3F)C(=O)NO

IUPAC InChI

InChI=1S/C19H16FN3O2/c1-12-21-10-15(11-22-12)13-6-8-14(9-7-13)18(19(24)23-25)16-4-2-3-5-17(16)20/h2-11,18,25H,1H3,(H,23,24)/t18-/m0/s1

IUPAC InChI key

SFXMVIQZYOMYOF-SFHVURJKSA-N
EBE

wwPDB Information

Atom count

41 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-03-13

Last modified at

2018-11-30

Status

Released

Obsoleted

Not Assigned



EBE : Atoms of Molecule

Total Number of Atoms: 41
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 N Y N 0 -0.084 -0.529 -0.711
2 C5 C C2 N Y N 0 1.283 -0.421 -0.867
3 C6 C C3 N Y N 0 2.087 -0.124 0.232
4 C7 C C4 N Y N 0 3.557 -0.006 0.069
5 C8 C C5 N Y N 0 4.158 -0.184 -1.179
6 C3 C C6 N Y N 0 -0.656 -0.342 0.534
7 C2 C C7 N Y N 0 0.136 -0.046 1.629
8 C10 C C8 N Y N 0 6.21 0.207 -0.223
9 C1 C C9 N Y N 0 1.504 0.064 1.484
10 C19 C C10 N Y N 0 -2.761 0.718 -1.423
11 C12 C C11 N Y N 0 4.378 0.292 1.16
12 C13 C C12 S N N 0 -2.15 -0.461 0.699
13 C14 C C13 N Y N 0 -2.828 0.662 -0.044
14 C18 C C14 N Y N 0 -3.378 1.751 -2.104
15 N9 N N1 N Y N 0 5.471 -0.07 -1.279
16 C20 C C15 N N N 0 -2.613 -1.782 0.143
17 C24 C C16 N N N 0 7.703 0.327 -0.388
18 O21 O O1 N N N 0 -1.81 -2.552 -0.339
19 N22 N N2 N N N 0 -3.92 -2.109 0.182
20 O23 O O2 N N N 0 -4.356 -3.351 -0.341
21 C17 C C17 N Y N 0 -4.067 2.726 -1.407
22 C16 C C18 N Y N 0 -4.139 2.669 -0.027
23 C15 C C19 N Y N 0 -3.517 1.638 0.656
24 F25 F F1 N N N 0 -3.588 1.581 2.004
25 N11 N N3 N Y N 0 5.683 0.388 0.971
26 H1 H H1 N N N 0 -0.707 -0.755 -1.563
27 H2 H H2 N N N 0 1.73 -0.568 -1.84
28 H3 H H3 N N N 0 3.559 -0.412 -2.048
29 H4 H H4 N N N 0 -0.317 0.099 2.599
30 H5 H H5 N N N 0 2.122 0.295 2.339
31 H6 H H6 N N N 0 -2.223 -0.043 -1.968
32 H7 H H7 N N N 0 3.953 0.442 2.142
33 H8 H H8 N N N 0 -2.405 -0.402 1.757
34 H9 H H9 N N N 0 -3.321 1.797 -3.181
35 H10 H H10 N N N 0 8.166 -0.647 -0.231
36 H11 H H11 N N N 0 7.93 0.679 -1.395
37 H12 H H12 N N N 0 8.093 1.037 0.341
38 H13 H H13 N N N 0 -4.563 -1.493 0.568
39 H14 H H14 N N N 0 -5.309 -3.495 -0.268
40 H15 H H15 N N N 0 -4.548 3.533 -1.94
41 H16 H H16 N N N 0 -4.677 3.431 0.517



EBE : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 F25 C15 F C sing 1.35 N N
2 C16 C15 C C doub 1.38 N Y
3 C16 C17 C C sing 1.38 N Y
4 C15 C14 C C sing 1.38 N Y
5 C17 C18 C C doub 1.38 N Y
6 C14 C13 C C sing 1.51 N N
7 C14 C19 C C doub 1.38 N Y
8 C13 C20 C C sing 1.51 N N
9 C13 C3 C C sing 1.51 N N
10 C18 C19 C C sing 1.38 N Y
11 N22 C20 N C sing 1.35 N N
12 N22 O23 N O sing 1.42 N N
13 C20 O21 C O doub 1.21 N N
14 C4 C3 C C doub 1.38 N Y
15 C4 C5 C C sing 1.38 N Y
16 C3 C2 C C sing 1.38 N Y
17 C5 C6 C C doub 1.39 N Y
18 C2 C1 C C doub 1.38 N Y
19 C6 C1 C C sing 1.39 N Y
20 C6 C7 C C sing 1.48 N N
21 C8 C7 C C doub 1.4 N Y
22 C8 N9 C N sing 1.32 N Y
23 C7 C12 C C sing 1.4 N Y
24 N9 C10 N C doub 1.32 N Y
25 C12 N11 C N doub 1.32 N Y
26 C10 N11 C N sing 1.32 N Y
27 C10 C24 C C sing 1.51 N N
28 C4 H1 C H sing 1.08 N N
29 C5 H2 C H sing 1.08 N N
30 C8 H3 C H sing 1.08 N N
31 C2 H4 C H sing 1.08 N N
32 C1 H5 C H sing 1.08 N N
33 C19 H6 C H sing 1.08 N N
34 C12 H7 C H sing 1.08 N N
35 C13 H8 C H sing 1.09 N N
36 C18 H9 C H sing 1.08 N N
37 C24 H10 C H sing 1.09 N N
38 C24 H11 C H sing 1.09 N N
39 C24 H12 C H sing 1.09 N N
40 N22 H13 N H sing 0.97 N N
41 O23 H14 O H sing 0.97 N N
42 C17 H15 C H sing 1.08 N N
43 C16 H16 C H sing 1.08 N N



EBE : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
EBE 6fyz Open in New Window Bound ligand 3 1