Chemical Components in the PDB

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E6E : Summary

Code

E6E

One-letter code

X

Molecule name

4-{4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl}-2-(1-{thieno[3,2-d]pyrimidin-4-yl}piperidin-4-yl)-1,2,4a,5,8,8a-hexahydrophthalazin-1-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 (4~{a}~{R},8~{a}~{R})-4-[4-methoxy-3-[(2-methoxyphenyl)methoxy]phenyl]-2-(1-thieno[3,2-d]pyrimidin-4-ylpiperidin-4-yl)-4~{a},5,8,8~{a}-tetrahydrophthalazin-1-one

Formula

C34 H35 N5 O4 S

Formal charge

0

Molecular weight

609.738 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COc1ccccc1COc2cc(ccc2OC)C3=NN(C4CCN(CC4)c5ncnc6ccsc56)C(=O)[CH]7CC=CC[CH]37
SMILES OpenEye OEToolkits 2.0.6 COc1ccccc1COc2cc(ccc2OC)C3=NN(C(=O)C4C3CC=CC4)C5CCN(CC5)c6c7c(ccs7)ncn6
Canonical SMILES CACTVS 3.385 COc1ccccc1COc2cc(ccc2OC)C3=NN(C4CCN(CC4)c5ncnc6ccsc56)C(=O)[C@@H]7CC=CC[C@@H]37
Canonical SMILES OpenEye OEToolkits 2.0.6 COc1ccccc1COc2cc(ccc2OC)C3=NN(C(=O)[C@H]4[C@H]3CC=CC4)C5CCN(CC5)c6c7c(ccs7)ncn6

IUPAC InChI

InChI=1S/C34H35N5O4S/c1-41-28-10-6-3-7-23(28)20-43-30-19-22(11-12-29(30)42-2)31-25-8-4-5-9-26(25)34(40)39(37-31)24-13-16-38(17-14-24)33-32-27(15-18-44-32)35-21-36-33/h3-7,10-12,15,18-19,21,24-26H,8-9,13-14,16-17,20H2,1-2H3/t25-,26-/m1/s1

IUPAC InChI key

FPUMGIJNOYNQAE-CLJLJLNGSA-N
E6E

wwPDB Information

Atom count

79 (44 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-02-20

Last modified at

2019-03-15

Status

Released

Obsoleted

Not Assigned



E6E : Atoms of Molecule

Total Number of Atoms: 79
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 -0.693 4.764 2.971
2 O1 O O1 N N N 0 -1.451 3.963 2.062
3 C2 C C2 N Y N 0 -2.449 4.581 1.379
4 C3 C C3 N Y N 0 -2.692 5.933 1.575
5 C4 C C4 N Y N 0 -3.708 6.559 0.879
6 C5 C C5 N Y N 0 -4.483 5.84 -0.012
7 C6 C C6 N Y N 0 -4.243 4.493 -0.209
8 C7 C C7 N Y N 0 -3.225 3.863 0.479
9 C8 C C8 N N N 0 -2.96 2.396 0.259
10 O2 O O2 N N N 0 -3.882 1.885 -0.705
11 C9 C C9 N Y N 0 -3.779 0.566 -1.02
12 C10 C C10 N Y N 0 -2.816 -0.216 -0.412
13 C11 C C11 N Y N 0 -2.716 -1.572 -0.734
14 C12 C C12 N N N 0 -1.691 -2.412 -0.087
15 N1 N N1 N N N 0 -0.509 -1.929 0.143
16 N2 N N2 N N N 0 0.483 -2.714 0.745
17 C13 C C13 N N N 0 1.896 -2.378 0.55
18 C14 C C14 N N N 0 2.234 -2.433 -0.942
19 C15 C C15 N N N 0 3.695 -2.023 -1.144
20 N3 N N3 N N N 0 3.899 -0.663 -0.627
21 C16 C C16 N Y N 0 5.177 -0.211 -0.911
22 N4 N N4 N Y N 0 6.034 -0.98 -1.571
23 C17 C C17 N Y N 0 7.254 -0.552 -1.844
24 N5 N N5 N Y N 0 7.682 0.632 -1.487
25 C18 C C18 N Y N 0 6.884 1.49 -0.811
26 C19 C C19 N Y N 0 7.152 2.787 -0.345
27 C20 C C20 N Y N 0 6.159 3.387 0.292
28 S1 S S1 N Y N 0 4.748 2.344 0.368
29 C21 C C21 N Y N 0 5.586 1.072 -0.511
30 C22 C C22 N N N 0 3.626 -0.597 0.815
31 C23 C C23 N N N 0 2.163 -0.965 1.075
32 C24 C C24 N N N 0 0.143 -3.778 1.503
33 O3 O O3 N N N 0 0.997 -4.425 2.072
34 C25 C C25 R N N 0 -1.311 -4.151 1.631
35 C26 C C26 N N N 0 -1.457 -5.651 1.888
36 C27 C C27 N N N 0 -2.9 -6.047 1.749
37 C28 C C28 N N N 0 -3.797 -5.326 1.154
38 C29 C C29 N N N 0 -3.522 -3.991 0.522
39 C30 C C30 R N N 0 -2.019 -3.825 0.311
40 C31 C C31 N Y N 0 -3.589 -2.131 -1.67
41 C32 C C32 N Y N 0 -4.548 -1.343 -2.273
42 C33 C C33 N Y N 0 -4.647 0.002 -1.953
43 O4 O O4 N N N 0 -5.597 0.772 -2.547
44 C34 C C34 N N N 0 -6.453 0.131 -3.494
45 H1 H H1 N N N 0 -1.357 5.176 3.731
46 H2 H H2 N N N 0 0.069 4.149 3.449
47 H3 H H3 N N N 0 -0.215 5.578 2.426
48 H4 H H4 N N N 0 -2.088 6.495 2.272
49 H5 H H5 N N N 0 -3.897 7.612 1.031
50 H6 H H6 N N N 0 -5.276 6.332 -0.555
51 H7 H H7 N N N 0 -4.85 3.933 -0.906
52 H8 H H8 N N N 0 -1.941 2.261 -0.105
53 H9 H H9 N N N 0 -3.083 1.859 1.2
54 H10 H H10 N N N 0 -2.142 0.22 0.312
55 H11 H H11 N N N 0 2.517 -3.092 1.091
56 H12 H H12 N N N 0 2.087 -3.447 -1.312
57 H13 H H13 N N N 0 1.585 -1.748 -1.487
58 H14 H H14 N N N 0 4.344 -2.716 -0.609
59 H15 H H15 N N N 0 3.935 -2.046 -2.207
60 H16 H H16 N N N 0 7.925 -1.206 -2.382
61 H17 H H17 N N N 0 8.108 3.265 -0.497
62 H18 H H18 N N N 0 6.209 4.382 0.709
63 H19 H H19 N N N 0 4.275 -1.297 1.34
64 H20 H H20 N N N 0 3.815 0.414 1.174
65 H21 H H21 N N N 0 1.513 -0.257 0.561
66 H22 H H22 N N N 0 1.965 -0.931 2.147
67 H23 H H23 N N N 0 -1.767 -3.58 2.44
68 H24 H H24 N N N 0 -0.858 -6.204 1.165
69 H25 H H25 N N N 0 -1.113 -5.882 2.897
70 H26 H H26 N N N 0 -3.209 -6.991 2.172
71 H27 H H27 N N N 0 -4.806 -5.71 1.109
72 H28 H H28 N N N 0 -4.036 -3.931 -0.438
73 H29 H H29 N N N 0 -3.884 -3.198 1.177
74 H30 H H30 N N N 0 -1.684 -4.514 -0.464
75 H31 H H31 N N N 0 -3.514 -3.178 -1.921
76 H32 H H32 N N N 0 -5.223 -1.776 -2.997
77 H33 H H33 N N N 0 -6.996 -0.678 -3.004
78 H34 H H34 N N N 0 -7.163 0.856 -3.892
79 H35 H H35 N N N 0 -5.854 -0.276 -4.309



E6E : Chemical Bonds

Total Number of Bonds: 85
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O3 C24 O C doub 1.21 N N
2 C27 C26 C C sing 1.5 N N
3 C27 C28 C C doub 1.3 N N
4 C26 C25 C C sing 1.53 N N
5 C28 C29 C C sing 1.5 N N
6 C24 C25 C C sing 1.51 N N
7 C24 N2 C N sing 1.35 N N
8 C15 N3 C N sing 1.47 N N
9 C15 C14 C C sing 1.53 N N
10 C13 C14 C C sing 1.53 N N
11 C13 N2 C N sing 1.47 N N
12 C13 C23 C C sing 1.53 N N
13 C25 C30 C C sing 1.53 N N
14 C22 N3 C N sing 1.47 N N
15 C22 C23 C C sing 1.53 N N
16 N3 C16 N C sing 1.39 N N
17 N2 N1 N N sing 1.4 N N
18 C29 C30 C C sing 1.53 N N
19 C30 C12 C C sing 1.5 N N
20 C16 N4 C N doub 1.33 N Y
21 C16 C21 C C sing 1.4 N Y
22 N4 C17 N C sing 1.32 N Y
23 C21 S1 C S sing 1.76 N Y
24 C21 C18 C C doub 1.4 N Y
25 S1 C20 S C sing 1.76 N Y
26 C17 N5 C N doub 1.31 N Y
27 N1 C12 N C doub 1.3 N N
28 C12 C11 C C sing 1.47 N N
29 C18 N5 C N sing 1.35 N Y
30 C18 C19 C C sing 1.4 N Y
31 C20 C19 C C doub 1.32 N Y
32 C11 C31 C C doub 1.4 N Y
33 C11 C10 C C sing 1.4 N Y
34 C31 C32 C C sing 1.38 N Y
35 C10 C9 C C doub 1.38 N Y
36 C1 O1 C O sing 1.43 N N
37 O1 C2 O C sing 1.36 N N
38 C3 C2 C C doub 1.39 N Y
39 C3 C4 C C sing 1.38 N Y
40 C2 C7 C C sing 1.39 N Y
41 C32 C33 C C doub 1.39 N Y
42 C9 C33 C C sing 1.39 N Y
43 C9 O2 C O sing 1.36 N N
44 C4 C5 C C doub 1.38 N Y
45 C7 C8 C C sing 1.51 N N
46 C7 C6 C C doub 1.38 N Y
47 C8 O2 C O sing 1.43 N N
48 C33 O4 C O sing 1.36 N N
49 C5 C6 C C sing 1.38 N Y
50 O4 C34 O C sing 1.43 N N
51 C1 H1 C H sing 1.09 N N
52 C1 H2 C H sing 1.09 N N
53 C1 H3 C H sing 1.09 N N
54 C3 H4 C H sing 1.08 N N
55 C4 H5 C H sing 1.08 N N
56 C5 H6 C H sing 1.08 N N
57 C6 H7 C H sing 1.08 N N
58 C8 H8 C H sing 1.09 N N
59 C8 H9 C H sing 1.09 N N
60 C10 H10 C H sing 1.08 N N
61 C13 H11 C H sing 1.09 N N
62 C14 H12 C H sing 1.09 N N
63 C14 H13 C H sing 1.09 N N
64 C15 H14 C H sing 1.09 N N
65 C15 H15 C H sing 1.09 N N
66 C17 H16 C H sing 1.08 N N
67 C19 H17 C H sing 1.08 N N
68 C20 H18 C H sing 1.08 N N
69 C22 H19 C H sing 1.09 N N
70 C22 H20 C H sing 1.09 N N
71 C23 H21 C H sing 1.09 N N
72 C23 H22 C H sing 1.09 N N
73 C25 H23 C H sing 1.09 N N
74 C26 H24 C H sing 1.09 N N
75 C26 H25 C H sing 1.09 N N
76 C27 H26 C H sing 1.08 N N
77 C28 H27 C H sing 1.08 N N
78 C29 H28 C H sing 1.09 N N
79 C29 H29 C H sing 1.09 N N
80 C30 H30 C H sing 1.09 N N
81 C31 H31 C H sing 1.08 N N
82 C32 H32 C H sing 1.08 N N
83 C34 H33 C H sing 1.09 N N
84 C34 H34 C H sing 1.09 N N
85 C34 H35 C H sing 1.09 N N



E6E : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
E6E 6ft0 Open in New Window Bound ligand 4 1