Chemical Components in the PDB

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JN2 : Summary

Code

JN2

One-letter code

X

Molecule name

3-(4-fluorophenyl)-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]benzamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 3-(4-fluorophenyl)-~{N}-[(2~{R},3~{R},4~{S},5~{S},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]benzamide

Formula

C19 H20 F N O6

Formal charge

0

Molecular weight

377.364 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 OC[CH]1O[CH](NC(=O)c2cccc(c2)c3ccc(F)cc3)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 2.0.7 c1cc(cc(c1)C(=O)NC2C(C(C(C(O2)CO)O)O)O)c3ccc(cc3)F
Canonical SMILES CACTVS 3.385 OC[C@H]1O[C@@H](NC(=O)c2cccc(c2)c3ccc(F)cc3)[C@H](O)[C@@H](O)[C@@H]1O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(cc(c1)C(=O)N[C@H]2[C@@H]([C@H]([C@@H]([C@H](O2)CO)O)O)O)c3ccc(cc3)F

IUPAC InChI

InChI=1S/C19H20FNO6/c20-13-6-4-10(5-7-13)11-2-1-3-12(8-11)18(26)21-19-17(25)16(24)15(23)14(9-22)27-19/h1-8,14-17,19,22-25H,9H2,(H,21,26)/t14-,15-,16+,17-,19-/m1/s1

IUPAC InChI key

ZNFXGMNTWYBCJQ-OGJJZOIMSA-N
JN2

wwPDB Information

Atom count

47 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-03-13

Last modified at

2019-04-05

Status

Released

Obsoleted

Not Assigned



JN2 : Atoms of Molecule

Total Number of Atoms: 47
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C2 C C1 N N N 0 -0.289 0.213 0.133
2 C4 C C2 N Y N 0 0.95 1.809 -1.324
3 C3 C C3 N Y N 0 0.975 0.752 -0.412
4 C9 C C4 N Y N 0 4.683 0.142 -0.119
5 C8 C C5 N Y N 0 2.196 0.206 -0.018
6 C13 C C6 N Y N 0 7.08 0.113 -0.252
7 C14 C C7 N Y N 0 5.871 0.655 -0.637
8 C7 C C8 N Y N 0 3.38 0.718 -0.535
9 C6 C C9 N Y N 0 3.342 1.774 -1.445
10 C10 C C10 N Y N 0 4.722 -0.916 0.786
11 C12 C C11 N Y N 0 7.114 -0.939 0.648
12 C11 C C12 N Y N 0 5.936 -1.452 1.166
13 C5 C C13 N Y N 0 2.131 2.312 -1.834
14 O2' O O1 N N N 0 -3.233 2.283 1.402
15 C2' C C14 R N N 0 -3.732 1.338 0.454
16 C3' C C15 S N N 0 -5.058 0.76 0.957
17 O3' O O2 N N N 0 -6.03 1.803 1.05
18 C4' C C16 S N N 0 -5.544 -0.308 -0.029
19 O4' O O3 N N N 0 -6.744 -0.905 0.468
20 C5' C C17 R N N 0 -4.463 -1.38 -0.181
21 C6' C C18 N N N 0 -4.916 -2.419 -1.209
22 O6' O O4 N N N 0 -3.961 -3.48 -1.267
23 O5' O O5 N N N 0 -3.248 -0.771 -0.622
24 C1' C C19 R N N 0 -2.721 0.201 0.282
25 N1 N N1 N N N 0 -1.468 0.739 -0.254
26 F15 F F1 N N N 0 8.3 -1.466 1.023
27 O2 O O6 N N N 0 -0.265 -0.707 0.927
28 H1 H H1 N N N 0 0.006 2.23 -1.635
29 H2 H H2 N N N 0 2.221 -0.612 0.688
30 H3 H H3 N N N 0 8.001 0.51 -0.654
31 H4 H H4 N N N 0 5.845 1.476 -1.339
32 H5 H H5 N N N 0 4.262 2.173 -1.847
33 H6 H H6 N N N 0 3.804 -1.316 1.19
34 H7 H H7 N N N 0 5.967 -2.273 1.867
35 H8 H H8 N N N 0 2.106 3.13 -2.539
36 H9 H H9 N N N 0 -2.391 2.687 1.149
37 H10 H H10 N N N 0 -3.89 1.832 -0.505
38 H11 H H11 N N N 0 -4.91 0.309 1.939
39 H12 H H12 N N N 0 -5.787 2.514 1.658
40 H13 H H13 N N N 0 -5.74 0.153 -0.997
41 H14 H H14 N N N 0 -7.471 -0.281 0.594
42 H15 H H15 N N N 0 -4.297 -1.868 0.78
43 H16 H H16 N N N 0 -5.887 -2.819 -0.918
44 H17 H H17 N N N 0 -4.996 -1.949 -2.19
45 H18 H H18 N N N 0 -4.184 -4.176 -1.9
46 H19 H H19 N N N 0 -2.532 -0.266 1.249
47 H20 H H20 N N N 0 -1.487 1.474 -0.887



JN2 : Chemical Bonds

Total Number of Bonds: 49
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3' C3' O C sing 1.43 N N
2 O4' C4' O C sing 1.43 N N
3 C3' C4' C C sing 1.53 N N
4 C3' C2' C C sing 1.53 N N
5 C4' C5' C C sing 1.53 N N
6 O2' C2' O C sing 1.43 N N
7 C2' C1' C C sing 1.53 N N
8 O6' C6' O C sing 1.43 N N
9 C5' C6' C C sing 1.53 N N
10 C5' O5' C O sing 1.43 N N
11 C1' O5' C O sing 1.43 N N
12 C1' N1 C N sing 1.47 N N
13 N1 C2 N C sing 1.35 N N
14 C2 O2 C O doub 1.22 N N
15 C2 C3 C C sing 1.48 N N
16 C4 C3 C C doub 1.4 N Y
17 C4 C5 C C sing 1.38 N Y
18 C3 C8 C C sing 1.39 N Y
19 C5 C6 C C doub 1.38 N Y
20 C8 C7 C C doub 1.39 N Y
21 C6 C7 C C sing 1.39 N Y
22 C7 C9 C C sing 1.48 N N
23 C9 C14 C C doub 1.39 N Y
24 C9 C10 C C sing 1.39 N Y
25 C14 C13 C C sing 1.38 N Y
26 C10 C11 C C doub 1.38 N Y
27 C13 C12 C C doub 1.38 N Y
28 C11 C12 C C sing 1.39 N Y
29 C12 F15 C F sing 1.35 N N
30 C4 H1 C H sing 1.08 N N
31 C8 H2 C H sing 1.08 N N
32 C13 H3 C H sing 1.08 N N
33 C14 H4 C H sing 1.08 N N
34 C6 H5 C H sing 1.08 N N
35 C10 H6 C H sing 1.08 N N
36 C11 H7 C H sing 1.08 N N
37 C5 H8 C H sing 1.08 N N
38 O2' H9 O H sing 0.97 N N
39 C2' H10 C H sing 1.09 N N
40 C3' H11 C H sing 1.09 N N
41 O3' H12 O H sing 0.97 N N
42 C4' H13 C H sing 1.09 N N
43 O4' H14 O H sing 0.97 N N
44 C5' H15 C H sing 1.09 N N
45 C6' H16 C H sing 1.09 N N
46 C6' H17 C H sing 1.09 N N
47 O6' H18 O H sing 0.97 N N
48 C1' H19 C H sing 1.09 N N
49 N1 H20 N H sing 0.97 N N



JN2 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
JN2 6r0h Open in New Window Bound ligand 1 1