Chemical Components in the PDB

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8W7 : Summary

Code

8W7

One-letter code

X

Molecule name

(3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione

Systematic names

ProgramVersionName
ACDLabs 12.01 (3S)-3-[4-({4-[(morpholin-4-yl)methyl]phenyl}methoxy)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione
OpenEye OEToolkits 2.0.6 (3~{S})-3-[7-[[4-(morpholin-4-ylmethyl)phenyl]methoxy]-3-oxidanylidene-1~{H}-isoindol-2-yl]piperidine-2,6-dione

Formula

C25 H27 N3 O5

Formal charge

0

Molecular weight

449.499 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 c1cc(c2c(c1)C(N(C2)C3C(NC(CC3)=O)=O)=O)OCc5ccc(CN4CCOCC4)cc5
SMILES CACTVS 3.385 O=C1CC[CH](N2Cc3c(OCc4ccc(CN5CCOCC5)cc4)cccc3C2=O)C(=O)N1
SMILES OpenEye OEToolkits 2.0.6 c1cc2c(c(c1)OCc3ccc(cc3)CN4CCOCC4)CN(C2=O)C5CCC(=O)NC5=O
Canonical SMILES CACTVS 3.385 O=C1CC[C@H](N2Cc3c(OCc4ccc(CN5CCOCC5)cc4)cccc3C2=O)C(=O)N1
Canonical SMILES OpenEye OEToolkits 2.0.6 c1cc2c(c(c1)OCc3ccc(cc3)CN4CCOCC4)CN(C2=O)[C@H]5CCC(=O)NC5=O

IUPAC InChI

InChI=1S/C25H27N3O5/c29-23-9-8-21(24(30)26-23)28-15-20-19(25(28)31)2-1-3-22(20)33-16-18-6-4-17(5-7-18)14-27-10-12-32-13-11-27/h1-7,21H,8-16H2,(H,26,29,30)/t21-/m0/s1

IUPAC InChI key

IXZOHGPZAQLIBH-NRFANRHFSA-N
8W7

wwPDB Information

Atom count

60 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-03-08

Last modified at

2017-04-28

Status

Released

Obsoleted

Not Assigned



8W7 : Atoms of Molecule

Total Number of Atoms: 60
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 -2.722 -4.259 0.219
2 C2 C C2 N Y N 0 -1.55 -3.526 0.213
3 C3 C C3 N Y N 0 -1.594 -2.14 0.125
4 C4 C C4 N Y N 0 -3.944 -3.622 0.133
5 C5 C C5 N Y N 0 -3.999 -2.23 0.044
6 C6 C C6 N Y N 0 -2.812 -1.495 0.044
7 N1 N N1 N N N 0 -4.674 -0.021 -0.11
8 N2 N N2 N N N 0 -4.018 3.082 -0.786
9 N3 N N3 N N N 0 6.5 0.772 0.222
10 O1 O O1 N N N 0 -6.301 -1.604 -0.081
11 C7 C C7 N N N 0 -3.208 -0.044 -0.06
12 C8 C C8 N N N 0 -5.128 -1.285 -0.058
13 C9 C C9 S N N 0 -5.506 1.181 -0.203
14 C10 C C10 N N N 0 -5.593 1.851 1.173
15 C11 C C11 N N N 0 -4.201 2.334 1.575
16 C12 C C12 N N N 0 -3.653 3.231 0.496
17 C13 C C13 N N N 0 -4.892 2.145 -1.184
18 C14 C C14 N N N 0 0.782 -2.155 0.206
19 C15 C C15 N Y N 0 1.946 -1.197 0.186
20 O2 O O2 N N N 0 -5.192 2.072 -2.356
21 C22 C C16 N N N 0 6.714 -0.049 -0.979
22 C23 C C17 N N N 0 8.004 -0.857 -0.814
23 O5 O O3 N N N 0 9.093 0.038 -0.569
24 C24 C C18 N N N 0 8.917 0.853 0.593
25 C25 C C19 N N N 0 7.636 1.678 0.443
26 C21 C C20 N N N 0 5.24 1.522 0.129
27 C20 C C21 N Y N 0 4.08 0.559 0.15
28 C19 C C22 N Y N 0 3.506 0.195 1.353
29 C17 C C23 N Y N 0 2.439 -0.684 1.371
30 C18 C C24 N Y N 0 3.59 0.042 -1.035
31 C16 C C25 N Y N 0 2.523 -0.836 -1.016
32 O4 O O4 N N N 0 -0.441 -1.421 0.119
33 O3 O O5 N N N 0 -2.867 4.104 0.793
34 H1 H H1 N N N 0 -2.682 -5.336 0.287
35 H2 H H2 N N N 0 -0.598 -4.032 0.276
36 H3 H H3 N N N 0 -4.856 -4.2 0.133
37 H4 H H4 N N N 0 -3.639 3.678 -1.451
38 H6 H H6 N N N 0 -2.855 0.497 0.819
39 H7 H H7 N N N 0 -2.795 0.401 -0.965
40 H8 H H8 N N N 0 -6.506 0.907 -0.539
41 H9 H H9 N N N 0 -6.269 2.705 1.122
42 H10 H H10 N N N 0 -5.963 1.135 1.906
43 H11 H H11 N N N 0 -4.264 2.882 2.515
44 H12 H H12 N N N 0 -3.539 1.477 1.695
45 H13 H H13 N N N 0 0.858 -2.836 -0.641
46 H14 H H14 N N N 0 0.798 -2.726 1.135
47 H15 H H15 N N N 0 5.873 -0.73 -1.109
48 H16 H H16 N N N 0 6.798 0.598 -1.852
49 H17 H H17 N N N 0 7.9 -1.542 0.027
50 H18 H H18 N N N 0 8.197 -1.423 -1.725
51 H19 H H19 N N N 0 8.84 0.217 1.475
52 H20 H H20 N N N 0 9.771 1.522 0.701
53 H24 H H24 N N N 0 5.223 2.091 -0.8
54 H21 H H21 N N N 0 7.735 2.352 -0.407
55 H22 H H22 N N N 0 7.469 2.257 1.351
56 H23 H H23 N N N 0 5.16 2.205 0.975
57 H28 H H28 N N N 0 2.141 -1.241 -1.942
58 H25 H H25 N N N 0 3.888 0.599 2.279
59 H26 H H26 N N N 0 1.99 -0.969 2.312
60 H27 H H27 N N N 0 4.039 0.327 -1.975



8W7 : Chemical Bonds

Total Number of Bonds: 64
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C11 C10 C C sing 1.53 N N
2 C11 C12 C C sing 1.51 N N
3 C10 C9 C C sing 1.53 N N
4 O3 C12 O C doub 1.21 N N
5 C12 N2 C N sing 1.34 N N
6 C9 N1 C N sing 1.46 N N
7 C9 C13 C C sing 1.51 N N
8 C7 N1 C N sing 1.47 N N
9 C7 C6 C C sing 1.51 N N
10 N1 C8 N C sing 1.34 N N
11 O4 C3 O C sing 1.36 N N
12 O4 C14 O C sing 1.43 N N
13 C6 C3 C C doub 1.38 N Y
14 C6 C5 C C sing 1.4 N Y
15 C8 O1 C O doub 1.22 N N
16 C8 C5 C C sing 1.48 N N
17 C3 C2 C C sing 1.39 N Y
18 C5 C4 C C doub 1.4 N Y
19 C2 C1 C C doub 1.38 N Y
20 C14 C15 C C sing 1.51 N N
21 N2 C13 N C sing 1.34 N N
22 C4 C1 C C sing 1.38 N Y
23 C13 O2 C O doub 1.21 N N
24 C15 C17 C C doub 1.38 N Y
25 C15 C16 C C sing 1.38 N Y
26 C17 C19 C C sing 1.38 N Y
27 C16 C18 C C doub 1.38 N Y
28 C19 C20 C C doub 1.38 N Y
29 C18 C20 C C sing 1.38 N Y
30 C20 C21 C C sing 1.51 N N
31 C21 N3 C N sing 1.47 N N
32 N3 C25 N C sing 1.47 N N
33 N3 C22 N C sing 1.47 N N
34 C25 C24 C C sing 1.53 N N
35 C24 O5 C O sing 1.43 N N
36 C22 C23 C C sing 1.53 N N
37 C23 O5 C O sing 1.43 N N
38 C1 H1 C H sing 1.08 N N
39 C2 H2 C H sing 1.08 N N
40 C4 H3 C H sing 1.08 N N
41 N2 H4 N H sing 0.97 N N
42 C7 H6 C H sing 1.09 N N
43 C7 H7 C H sing 1.09 N N
44 C9 H8 C H sing 1.09 N N
45 C10 H9 C H sing 1.09 N N
46 C10 H10 C H sing 1.09 N N
47 C11 H11 C H sing 1.09 N N
48 C11 H12 C H sing 1.09 N N
49 C14 H13 C H sing 1.09 N N
50 C14 H14 C H sing 1.09 N N
51 C22 H15 C H sing 1.09 N N
52 C22 H16 C H sing 1.09 N N
53 C23 H17 C H sing 1.09 N N
54 C23 H18 C H sing 1.09 N N
55 C24 H19 C H sing 1.09 N N
56 C24 H20 C H sing 1.09 N N
57 C25 H21 C H sing 1.09 N N
58 C25 H22 C H sing 1.09 N N
59 C21 H23 C H sing 1.09 N N
60 C21 H24 C H sing 1.09 N N
61 C19 H25 C H sing 1.08 N N
62 C17 H26 C H sing 1.08 N N
63 C18 H27 C H sing 1.08 N N
64 C16 H28 C H sing 1.08 N N



8W7 : Used in PDB Entries

Total Number of PDB Entries: 4
Ligand Code PDB Entry ID Type Total Distinct
8W7 5v3o Open in New Window Bound ligand 1 1
8W7 7ps9 Open in New Window Bound ligand 3 1
8W7 8d80 Open in New Window Bound ligand 1 1
8W7 8u15 Open in New Window Bound ligand 2 1