Chemical Components in the PDB

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SO0 : Summary

Code

SO0

One-letter code

X

Molecule name

(1S,3aR,6aS)-2-[(2,4-dichlorophenoxy)acetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}octahydrocyclopenta[c]pyrrole-1-carboxamide

Systematic names

ProgramVersionName
ACDLabs 12.01 (1S,3aR,6aS)-2-[(2,4-dichlorophenoxy)acetyl]-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}octahydrocyclopenta[c]pyrrole-1-carboxamide
OpenEye OEToolkits 2.0.7 (3~{S},3~{a}~{S},6~{a}~{R})-2-[2-[2,4-bis(chloranyl)phenoxy]ethanoyl]-~{N}-[(2~{S})-1-oxidanyl-3-[(3~{S})-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]-3,3~{a},4,5,6,6~{a}-hexahydro-1~{H}-cyclopenta[c]pyrrole-3-carboxamide

Formula

C23 H29 Cl2 N3 O5

Formal charge

0

Molecular weight

498.399 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1NCCC1CC(CO)NC(=O)C1C2CCCC2CN1C(=O)COc1ccc(Cl)cc1Cl
SMILES CACTVS 3.385 OC[CH](C[CH]1CCNC1=O)NC(=O)[CH]2[CH]3CCC[CH]3CN2C(=O)COc4ccc(Cl)cc4Cl
SMILES OpenEye OEToolkits 2.0.7 c1cc(c(cc1Cl)Cl)OCC(=O)N2CC3CCCC3C2C(=O)NC(CC4CCNC4=O)CO
Canonical SMILES CACTVS 3.385 OC[C@H](C[C@@H]1CCNC1=O)NC(=O)[C@@H]2[C@H]3CCC[C@H]3CN2C(=O)COc4ccc(Cl)cc4Cl
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc(c(cc1Cl)Cl)OCC(=O)N2C[C@@H]3CCC[C@@H]3[C@H]2C(=O)N[C@@H](C[C@@H]4CCNC4=O)CO

IUPAC InChI

InChI=1S/C23H29Cl2N3O5/c24-15-4-5-19(18(25)9-15)33-12-20(30)28-10-14-2-1-3-17(14)21(28)23(32)27-16(11-29)8-13-6-7-26-22(13)31/h4-5,9,13-14,16-17,21,29H,1-3,6-8,10-12H2,(H,26,31)(H,27,32)/t13-,14-,16-,17-,21-/m0/s1

IUPAC InChI key

WFNOKGZUZOGKBO-ZEAPZOAHSA-N
SO0

wwPDB Information

Atom count

62 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2023-08-28

Last modified at

2024-08-23

Status

Released

Obsoleted

Not Assigned



SO0 : Atoms of Molecule

Total Number of Atoms: 62
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 1.408 -5.059 0.262
2 C10 C C2 N N N 0 1.822 -4.81 1.725
3 C11 C C3 N N N 0 -2.012 -0.804 0.137
4 C15 C C7 N N N 0 2.344 -0.567 -0.691
5 C12 C C4 N N N 0 -0.538 -0.526 0.28
6 C13 C C5 N N N 0 0.001 -2.975 0.175
7 C14 C C6 S N N 0 1.799 -1.418 0.427
8 C16 C C8 R N N 0 1.28 -3.654 -0.361
9 C17 C C9 S N N 0 4.095 0.819 -1.666
10 C19 C C10 N N N 0 5.125 1.801 -1.104
11 C2 C C11 N N N 0 2.473 -3.419 1.77
12 C20 C C12 S N N 0 4.432 2.778 -0.152
13 C21 C C13 N N N 0 5.448 3.801 0.407
14 C22 C C14 N N N 0 5.872 3.132 1.733
15 C24 C C15 N N N 0 3.925 2.052 1.074
16 C3 C C16 N Y N 0 -4.085 0.356 0.03
17 C6 C C20 N Y N 0 -6.838 0.206 -0.217
18 C34 C C17 S N N 0 2.402 -2.835 0.347
19 C4 C C18 N Y N 0 -4.704 -0.878 -0.099
20 C5 C C19 N Y N 0 -6.079 -0.951 -0.222
21 C7 C C21 N Y N 0 -6.222 1.439 -0.088
22 C8 C C22 N N N 0 4.762 -0.078 -2.711
23 C9 C C23 N Y N 0 -4.849 1.516 0.041
24 N13 N N1 N N N 0 0.342 -1.546 0.293
25 N16 N N2 N N N 0 3.565 -0.009 -0.579
26 N23 N N3 N N N 0 4.746 2.272 2.115
27 O1 O O1 N N N 0 -2.733 0.43 0.15
28 O26 O O2 N N N 0 2.922 1.371 1.113
29 O33 O O3 N N N 0 -0.144 0.616 0.384
30 O38 O O4 N N N 0 1.683 -0.384 -1.691
31 O9 O O5 N N N 0 5.902 -0.717 -2.132
32 CL1 CL CL1 N N N 0 -4.077 3.063 0.203
33 CL2 CL CL2 N N N 0 -8.564 0.111 -0.372
34 H1 H H1 N N N 0 2.176 -5.634 -0.256
35 H2 H H2 N N N 0 0.453 -5.582 0.222
36 H3 H H3 N N N 0 0.943 -4.832 2.369
37 H4 H H4 N N N 0 2.537 -5.568 2.044
38 H7 H H7 N N N 0 -0.822 -3.11 -0.526
39 H5 H H5 N N N 0 -2.194 -1.32 -0.806
40 H6 H H6 N N N 0 -2.346 -1.429 0.964
41 H8 H H8 N N N 0 -0.262 -3.382 1.151
42 H9 H H9 N N N 0 2.043 -0.966 1.388
43 H10 H H10 N N N 0 1.351 -3.644 -1.449
44 H11 H H11 N N N 0 3.28 1.374 -2.13
45 H12 H H12 N N N 0 5.894 1.25 -0.563
46 H13 H H13 N N N 0 5.584 2.355 -1.923
47 H14 H H14 N N N 0 1.928 -2.777 2.462
48 H15 H H15 N N N 0 3.512 -3.507 2.086
49 H16 H H16 N N N 0 3.614 3.288 -0.66
50 H17 H H17 N N N 0 6.3 3.911 -0.264
51 H18 H H18 N N N 0 4.971 4.764 0.59
52 H19 H H19 N N N 0 6.771 2.533 1.583
53 H20 H H20 N N N 0 6.046 3.889 2.498
54 H21 H H21 N N N 0 3.354 -2.863 -0.183
55 H22 H H22 N N N 0 -4.113 -1.781 -0.105
56 H23 H H23 N N N 0 -6.561 -1.912 -0.323
57 H24 H H24 N N N 0 -6.817 2.34 -0.079
58 H25 H H25 N N N 0 4.052 -0.834 -3.046
59 H26 H H26 N N N 0 5.077 0.527 -3.561
60 H27 H H27 N N N 0 4.094 -0.154 0.221
61 H28 H H28 N N N 0 4.612 1.909 3.005
62 H29 H H29 N N N 0 6.375 -1.302 -2.74



SO0 : Chemical Bonds

Total Number of Bonds: 65
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CL1 C9 CL C sing 1.74 N N
2 C7 C9 C C doub 1.38 N Y
3 C7 C6 C C sing 1.38 N Y
4 CL2 C6 CL C sing 1.74 N N
5 C9 C3 C C sing 1.39 N Y
6 C6 C5 C C doub 1.38 N Y
7 C13 C16 C C sing 1.54 N N
8 C13 N13 C N sing 1.47 N N
9 C16 C34 C C sing 1.56 N N
10 C16 C1 C C sing 1.54 N N
11 O38 C15 O C doub 1.21 N N
12 C3 O1 C O sing 1.36 N N
13 C3 C4 C C doub 1.39 N Y
14 C11 O1 C O sing 1.43 N N
15 C11 C12 C C sing 1.51 N N
16 C5 C4 C C sing 1.38 N Y
17 C34 C14 C C sing 1.54 N N
18 C34 C2 C C sing 1.54 N N
19 N13 C12 N C sing 1.35 N N
20 N13 C14 N C sing 1.47 N N
21 C1 C10 C C sing 1.54 N N
22 C12 O33 C O doub 1.21 N N
23 C15 C14 C C sing 1.51 N N
24 C15 N16 C N sing 1.35 N N
25 C21 C22 C C sing 1.54 N N
26 C21 C20 C C sing 1.55 N N
27 C2 C10 C C sing 1.54 N N
28 C22 N23 C N sing 1.47 N N
29 C17 N16 C N sing 1.47 N N
30 C17 C8 C C sing 1.53 N N
31 C17 C19 C C sing 1.53 N N
32 O9 C8 O C sing 1.43 N N
33 C20 C19 C C sing 1.53 N N
34 C20 C24 C C sing 1.51 N N
35 N23 C24 N C sing 1.34 N N
36 C24 O26 C O doub 1.21 N N
37 C1 H1 C H sing 1.09 N N
38 C1 H2 C H sing 1.09 N N
39 C10 H3 C H sing 1.09 N N
40 C10 H4 C H sing 1.09 N N
41 C11 H5 C H sing 1.09 N N
42 C11 H6 C H sing 1.09 N N
43 C13 H7 C H sing 1.09 N N
44 C13 H8 C H sing 1.09 N N
45 C14 H9 C H sing 1.09 N N
46 C16 H10 C H sing 1.09 N N
47 C17 H11 C H sing 1.09 N N
48 C19 H12 C H sing 1.09 N N
49 C19 H13 C H sing 1.09 N N
50 C2 H14 C H sing 1.09 N N
51 C2 H15 C H sing 1.09 N N
52 C20 H16 C H sing 1.09 N N
53 C21 H17 C H sing 1.09 N N
54 C21 H18 C H sing 1.09 N N
55 C22 H19 C H sing 1.09 N N
56 C22 H20 C H sing 1.09 N N
57 C34 H21 C H sing 1.09 N N
58 C4 H22 C H sing 1.08 N N
59 C5 H23 C H sing 1.08 N N
60 C7 H24 C H sing 1.08 N N
61 C8 H25 C H sing 1.09 N N
62 C8 H26 C H sing 1.09 N N
63 N16 H27 N H sing 0.97 N N
64 N23 H28 N H sing 0.97 N N
65 O9 H29 O H sing 0.97 N N



SO0 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
SO0 8ty4 Open in New Window Bound ligand 1 1