Chemical Components in the PDB

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IJS : Summary

Code

IJS

One-letter code

X

Molecule name

(3~{R},5~{R})-3-[2-[[methyl(prop-2-ynyl)amino]methyl]-1,3-thiazol-4-yl]-5-[3-[2-nitro-4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]pyrrolidin-3-ol

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (3~{R},5~{R})-3-[2-[[methyl(prop-2-ynyl)amino]methyl]-1,3-thiazol-4-yl]-5-[3-[2-nitro-4-(trifluoromethyl)phenyl]-1,2,4-oxadiazol-5-yl]pyrrolidin-3-ol

Formula

C21 H19 F3 N6 O4 S

Formal charge

0

Molecular weight

508.474 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN(CC#C)Cc1scc(n1)[C]2(O)CN[CH](C2)c3onc(n3)c4ccc(cc4[N](=O)=O)C(F)(F)F
SMILES OpenEye OEToolkits 2.0.7 CN(CC#C)Cc1nc(cs1)C2(CC(NC2)c3nc(no3)c4ccc(cc4N(=O)=O)C(F)(F)F)O
Canonical SMILES CACTVS 3.385 CN(CC#C)Cc1scc(n1)[C@]2(O)CN[C@H](C2)c3onc(n3)c4ccc(cc4[N](=O)=O)C(F)(F)F
Canonical SMILES OpenEye OEToolkits 2.0.7 CN(CC#C)Cc1nc(cs1)[C@]2(C[C@@H](NC2)c3nc(no3)c4ccc(cc4N(=O)=O)C(F)(F)F)O

IUPAC InChI

InChI=1S/C21H19F3N6O4S/c1-3-6-29(2)9-17-26-16(10-35-17)20(31)8-14(25-11-20)19-27-18(28-34-19)13-5-4-12(21(22,23)24)7-15(13)30(32)33/h1,4-5,7,10,14,25,31H,6,8-9,11H2,2H3/t14-,20-/m1/s1

IUPAC InChI key

COBDFCAWUNRFOD-JLTOFOAXSA-N
IJS

wwPDB Information

Atom count

54 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-08-01

Last modified at

2024-08-02

Status

Released

Obsoleted

Not Assigned



IJS : Atoms of Molecule

Total Number of Atoms: 54
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C15 C C1 N Y N 0 0.272 1.441 -0.105
2 C17 C C2 N Y N 0 2.289 0.875 0.217
3 C18 C C3 N Y N 0 3.562 0.112 0.242
4 C19 C C4 N Y N 0 3.613 -1.142 0.848
5 C14 C C5 R N N 0 -1.182 1.47 -0.503
6 C10 C C6 R N N 0 -3.279 2.303 0.449
7 C01 C C7 N N N 0 -6.2 -5.836 0.267
8 C02 C C8 N N N 0 -6.368 -4.868 -0.376
9 C03 C C9 N N N 0 -6.579 -3.655 -1.183
10 C05 C C10 N N N 0 -4.507 -2.638 -0.449
11 C06 C C11 N N N 0 -6.359 -1.244 -1.151
12 C07 C C12 N Y N 0 -5.924 -0.083 -0.294
13 C09 C C13 N Y N 0 -4.564 1.516 0.444
14 C12 C C14 N N N 0 -2.999 2.881 -0.955
15 C20 C C15 N Y N 0 4.8 -1.847 0.869
16 C21 C C16 N Y N 0 5.936 -1.312 0.29
17 C22 C C17 N N N 0 7.228 -2.087 0.317
18 C26 C C18 N Y N 0 5.89 -0.068 -0.313
19 C27 C C19 N Y N 0 4.708 0.643 -0.345
20 C33 C C20 N N N 0 -2.084 1.375 0.747
21 C34 C C21 N Y N 0 -5.575 1.778 1.279
22 F23 F F1 N N N 0 7.028 -3.305 0.975
23 F24 F F2 N N N 0 7.653 -2.329 -0.994
24 F25 F F3 N N N 0 8.203 -1.346 0.994
25 N04 N N1 N N N 0 -5.969 -2.504 -0.504
26 N08 N N2 N Y N 0 -4.785 0.515 -0.384
27 N13 N N3 N N N 0 -1.526 2.779 -1.115
28 N16 N N4 N Y N 0 1.112 0.455 -0.299
29 N28 N N5 N N N 0 4.66 1.972 -0.996
30 N31 N N6 N Y N 0 2.098 2.08 0.685
31 O11 O O1 N N N 0 -3.345 3.354 1.415
32 O29 O O2 N N N 0 5.686 2.49 -1.399
33 O30 O O3 N N N 0 3.594 2.546 -1.128
34 O32 O O4 N Y N 0 0.947 2.419 0.506
35 S35 S S1 N Y N 0 -6.872 0.636 0.934
36 H191 H H1 N N N 0 2.727 -1.56 1.301
37 H141 H H2 N N N 0 -1.402 0.657 -1.195
38 H011 H H3 N N N 0 -6.049 -6.701 0.842
39 H032 H H4 N N N 0 -6.118 -3.785 -2.162
40 H031 H H5 N N N 0 -7.648 -3.481 -1.305
41 H053 H H6 N N N 0 -4.087 -1.808 0.119
42 H051 H H7 N N N 0 -4.247 -3.579 0.035
43 H052 H H8 N N N 0 -4.104 -2.626 -1.462
44 H061 H H9 N N N 0 -7.441 -1.219 -1.275
45 H062 H H10 N N N 0 -5.88 -1.174 -2.128
46 H122 H H11 N N N 0 -3.506 2.289 -1.718
47 H121 H H12 N N N 0 -3.318 3.921 -1.009
48 H201 H H13 N N N 0 4.84 -2.819 1.339
49 H261 H H14 N N N 0 6.78 0.345 -0.764
50 H332 H H15 N N N 0 -2.426 0.35 0.889
51 H331 H H16 N N N 0 -1.546 1.722 1.629
52 H341 H H17 N N N 0 -5.595 2.554 2.029
53 H2 H H19 N N N 0 -1.265 2.803 -2.089
54 H111 H H21 N N N 0 -4.065 3.982 1.266



IJS : Chemical Bonds

Total Number of Bonds: 57
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C02 C01 C C trip 1.17 N N
2 C03 C02 C C sing 1.47 N N
3 N04 C03 N C sing 1.47 N N
4 C05 N04 C N sing 1.47 N N
5 C06 N04 C N sing 1.47 N N
6 C07 C06 C C sing 1.51 N N
7 N08 C07 N C doub 1.29 N Y
8 C09 N08 C N sing 1.32 N Y
9 O11 C10 O C sing 1.43 N N
10 C12 C10 C C sing 1.54 N N
11 N13 C12 N C sing 1.49 N N
12 C14 N13 C N sing 1.49 N N
13 N16 C15 N C doub 1.31 N Y
14 C17 N16 C N sing 1.35 N Y
15 C19 C18 C C doub 1.39 N Y
16 C20 C19 C C sing 1.38 N Y
17 C21 C20 C C doub 1.38 N Y
18 F23 C22 F C sing 1.4 N N
19 F24 C22 F C sing 1.4 N N
20 F25 C22 F C sing 1.4 N N
21 C22 C21 C C sing 1.51 N N
22 C26 C21 C C sing 1.38 N Y
23 C27 C26 C C doub 1.38 N Y
24 N28 C27 N C sing 1.48 N N
25 O29 N28 O N doub 1.22 N N
26 O30 N28 O N doub 1.22 N N
27 C18 C17 C C sing 1.48 N N
28 N31 C17 N C doub 1.31 N Y
29 O32 N31 O N sing 1.21 N Y
30 C15 C14 C C sing 1.51 N N
31 C33 C14 C C sing 1.54 N N
32 C10 C09 C C sing 1.51 N N
33 C34 C09 C C doub 1.34 N Y
34 S35 C34 S C sing 1.76 N Y
35 C07 S35 C S sing 1.71 N Y
36 C10 C33 C C sing 1.54 N N
37 C15 O32 C O sing 1.34 N Y
38 C18 C27 C C sing 1.39 N Y
39 C19 H191 C H sing 1.08 N N
40 C14 H141 C H sing 1.09 N N
41 C01 H011 C H sing 1.05 N N
42 C03 H032 C H sing 1.09 N N
43 C03 H031 C H sing 1.09 N N
44 C05 H053 C H sing 1.09 N N
45 C05 H051 C H sing 1.09 N N
46 C05 H052 C H sing 1.09 N N
47 C06 H061 C H sing 1.09 N N
48 C06 H062 C H sing 1.09 N N
49 C12 H122 C H sing 1.09 N N
50 C12 H121 C H sing 1.09 N N
51 C20 H201 C H sing 1.08 N N
52 C26 H261 C H sing 1.08 N N
53 C33 H332 C H sing 1.09 N N
54 C33 H331 C H sing 1.09 N N
55 C34 H341 C H sing 1.08 N N
56 N13 H2 N H sing 1.01 N N
57 O11 H111 O H sing 0.97 N N



IJS : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
IJS 8q14 Open in New Window Bound ligand 1 1