Chemical Components in the PDB

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VFN : Summary

Code

VFN

One-letter code

X

Molecule name

~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]ethanamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 ~{N}-[(5-azanyl-1,3,4-oxadiazol-2-yl)methyl]-2-(2-chlorophenyl)sulfanyl-~{N}-[(4-cyanophenyl)methyl]ethanamide

Formula

C19 H16 Cl N5 O2 S

Formal charge

0

Molecular weight

413.881 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Nc1oc(CN(Cc2ccc(cc2)C#N)C(=O)CSc3ccccc3Cl)nn1
SMILES OpenEye OEToolkits 2.0.7 c1ccc(c(c1)SCC(=O)N(Cc2ccc(cc2)C#N)Cc3nnc(o3)N)Cl
Canonical SMILES CACTVS 3.385 Nc1oc(CN(Cc2ccc(cc2)C#N)C(=O)CSc3ccccc3Cl)nn1
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc(c(c1)SCC(=O)N(Cc2ccc(cc2)C#N)Cc3nnc(o3)N)Cl

IUPAC InChI

InChI=1S/C19H16ClN5O2S/c20-15-3-1-2-4-16(15)28-12-18(26)25(11-17-23-24-19(22)27-17)10-14-7-5-13(9-21)6-8-14/h1-8H,10-12H2,(H2,22,24)

IUPAC InChI key

DDHNQWBEECYOFY-UHFFFAOYSA-N
VFN

wwPDB Information

Atom count

44 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-05-18

Last modified at

2021-10-08

Status

Released

Obsoleted

Not Assigned



VFN : Atoms of Molecule

Total Number of Atoms: 44
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C15 C C1 N N N 0 -6.37 -2.833 0.992
2 C23 C C2 N Y N 0 4.559 -0.259 2.222
3 C24 C C3 N Y N 0 5.645 -1.077 1.969
4 C11 C C4 N Y N 0 -4.547 -2.287 -0.554
5 C13 C C5 N Y N 0 -5.385 -0.589 0.944
6 C10 C C6 N Y N 0 -3.647 -1.378 -1.069
7 C14 C C7 N Y N 0 -4.483 0.311 0.417
8 C22 C C8 N Y N 0 3.444 -0.317 1.41
9 C25 C C9 N Y N 0 5.622 -1.951 0.898
10 C12 C C10 N Y N 0 -5.428 -1.897 0.457
11 C9 C C11 N Y N 0 -3.614 -0.083 -0.585
12 C21 C C12 N Y N 0 3.416 -1.194 0.333
13 C26 C C13 N Y N 0 4.512 -2.011 0.077
14 C5 C C14 N Y N 0 -0.588 3.027 0.342
15 C2 C C15 N Y N 0 0.83 4.572 -0.155
16 C17 C C16 N N N 0 -0.401 0.008 -0.757
17 C8 C C17 N N N 0 -2.631 0.906 -1.157
18 C6 C C18 N N N 0 -1.204 1.722 0.777
19 C19 C C19 N N N 0 0.881 -0.046 0.032
20 N16 N N1 N N N 0 -7.117 -3.576 1.416
21 N4 N N2 N Y N 0 -1.23 4.096 -0.026
22 N3 N N3 N Y N 0 -0.389 5.023 -0.324
23 N1 N N4 N N N 0 2.001 5.274 -0.373
24 N7 N N5 N N N 0 -1.384 0.854 -0.389
25 O18 O O1 N N N 0 -0.55 -0.711 -1.723
26 O28 O O2 N Y N 0 0.73 3.299 0.27
27 S20 S S1 N N N 0 1.995 -1.272 -0.707
28 CL1 CL CL1 N N N 0 4.483 -3.109 -1.267
29 H1 H H1 N N N 0 4.581 0.422 3.06
30 H2 H H2 N N N 0 6.514 -1.032 2.609
31 H3 H H3 N N N 0 -4.575 -3.298 -0.935
32 H4 H H4 N N N 0 -6.063 -0.28 1.726
33 H5 H H5 N N N 0 -2.965 -1.679 -1.851
34 H6 H H6 N N N 0 -4.449 1.323 0.793
35 H7 H H7 N N N 0 2.594 0.318 1.611
36 H8 H H8 N N N 0 6.472 -2.587 0.702
37 H9 H H9 N N N 0 -2.428 0.656 -2.198
38 H10 H H10 N N N 0 -3.051 1.911 -1.099
39 H11 H H11 N N N 0 -0.549 1.233 1.497
40 H12 H H12 N N N 0 -2.173 1.914 1.239
41 H13 H H13 N N N 0 1.359 0.934 0.017
42 H14 H H14 N N N 0 0.663 -0.327 1.062
43 H15 H H15 N N N 0 1.965 6.193 -0.683
44 H16 H H16 N N N 0 2.858 4.848 -0.218



VFN : Chemical Bonds

Total Number of Bonds: 46
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CL1 C26 CL C sing 1.74 N N
2 S20 C21 S C sing 1.76 N N
3 S20 C19 S C sing 1.81 N N
4 C26 C21 C C doub 1.39 N Y
5 C26 C25 C C sing 1.38 N Y
6 C21 C22 C C sing 1.39 N Y
7 O18 C17 O C doub 1.21 N N
8 C19 C17 C C sing 1.51 N N
9 C25 C24 C C doub 1.38 N Y
10 C17 N7 C N sing 1.35 N N
11 C22 C23 C C doub 1.38 N Y
12 N7 C8 N C sing 1.47 N N
13 N7 C6 N C sing 1.46 N N
14 C24 C23 C C sing 1.38 N Y
15 C8 C9 C C sing 1.51 N N
16 C6 C5 C C sing 1.51 N N
17 C9 C14 C C doub 1.38 N Y
18 C9 C10 C C sing 1.38 N Y
19 C14 C13 C C sing 1.38 N Y
20 C5 O28 C O sing 1.35 N Y
21 C5 N4 C N doub 1.3 N Y
22 O28 C2 O C sing 1.35 N Y
23 C10 C11 C C doub 1.38 N Y
24 C13 C12 C C doub 1.4 N Y
25 N4 N3 N N sing 1.29 N Y
26 C2 N1 C N sing 1.38 N N
27 C2 N3 C N doub 1.31 N Y
28 C11 C12 C C sing 1.4 N Y
29 C12 C15 C C sing 1.43 N N
30 C15 N16 C N trip 1.14 N N
31 C23 H1 C H sing 1.08 N N
32 C24 H2 C H sing 1.08 N N
33 C11 H3 C H sing 1.08 N N
34 C13 H4 C H sing 1.08 N N
35 C10 H5 C H sing 1.08 N N
36 C14 H6 C H sing 1.08 N N
37 C22 H7 C H sing 1.08 N N
38 C25 H8 C H sing 1.08 N N
39 C8 H9 C H sing 1.09 N N
40 C8 H10 C H sing 1.09 N N
41 C6 H11 C H sing 1.09 N N
42 C6 H12 C H sing 1.09 N N
43 C19 H13 C H sing 1.09 N N
44 C19 H14 C H sing 1.09 N N
45 N1 H15 N H sing 0.97 N N
46 N1 H16 N H sing 0.97 N N



VFN : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
VFN 7ok1 Open in New Window Bound ligand 3 1
VFN 7ok2 Open in New Window Bound ligand 30 1