Chemical Components in the PDB

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6PD : Summary

Code

6PD

One-letter code

X

Molecule name

[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]-[4-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]carbonyl-3-[[4-(pyrrolidin-1-ylmethoxy)phenyl]amino]phenyl]methanone

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 [4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]-[4-[4-(2-pyrrolidin-1-ylethyl)piperidin-1-yl]carbonyl-3-[[4-(pyrrolidin-1-ylmethoxy)phenyl]amino]phenyl]methanone

Formula

C41 H60 N6 O3

Formal charge

0

Molecular weight

684.953 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 O=C(N1CC[CH](CCN2CCCC2)CC1)c3ccc(C(=O)N4CC[CH](CCN5CCCC5)CC4)c(Nc6ccc(OCN7CCCC7)cc6)c3
SMILES OpenEye OEToolkits 2.0.6 c1cc(ccc1Nc2cc(ccc2C(=O)N3CCC(CC3)CCN4CCCC4)C(=O)N5CCC(CC5)CCN6CCCC6)OCN7CCCC7
Canonical SMILES CACTVS 3.385 O=C(N1CC[C@H](CCN2CCCC2)CC1)c3ccc(C(=O)N4CC[C@@H](CCN5CCCC5)CC4)c(Nc6ccc(OCN7CCCC7)cc6)c3
Canonical SMILES OpenEye OEToolkits 2.0.6 c1cc(ccc1Nc2cc(ccc2C(=O)N3CCC(CC3)CCN4CCCC4)C(=O)N5CCC(CC5)CCN6CCCC6)OCN7CCCC7

IUPAC InChI

InChI=1S/C41H60N6O3/c48-40(46-27-15-33(16-28-46)13-25-43-19-1-2-20-43)35-7-12-38(41(49)47-29-17-34(18-30-47)14-26-44-21-3-4-22-44)39(31-35)42-36-8-10-37(11-9-36)50-32-45-23-5-6-24-45/h7-12,31,33-34,42H,1-6,13-30,32H2

IUPAC InChI key

LPCWQWNRCGWRFC-UHFFFAOYSA-N
6PD

wwPDB Information

Atom count

110 (50 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-05-18

Last modified at

2017-05-19

Status

Released

Obsoleted

Not Assigned



6PD : Atoms of Molecule

Total Number of Atoms: 110
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C13 C C1 N N N 0 6.192 1.141 -0.37
2 C15 C C2 N N N 0 5.52 2.73 1.437
3 C17 C C3 N N N 0 8.598 0.688 -0.87
4 C20 C C4 N N N 0 10.791 -1.312 -3.082
5 C21 C C5 N N N 0 11.794 -0.762 -2.047
6 C22 C C6 N N N 0 10.96 0.159 -1.131
7 C26 C C7 N Y N 0 -2.18 3.136 0.87
8 C28 C C8 N Y N 0 -4.071 4.129 -0.219
9 O01 O O1 N N N 0 -2.834 0.258 2.446
10 C02 C C9 N N N 0 -1.92 -0.106 1.731
11 C03 C C10 N Y N 0 -0.584 0.507 1.872
12 C04 C C11 N Y N 0 -0.067 1.311 0.845
13 C05 C C12 N Y N 0 1.19 1.885 0.984
14 C06 C C13 N Y N 0 1.931 1.66 2.14
15 C07 C C14 N Y N 0 1.413 0.859 3.161
16 C08 C C15 N Y N 0 0.166 0.292 3.032
17 C09 C C16 N N N 0 3.272 2.271 2.289
18 N10 N N1 N N N 0 4.154 2.214 1.272
19 C11 C C17 N N N 0 3.769 1.637 -0.023
20 C12 C C18 N N N 0 4.781 0.55 -0.399
21 C14 C C19 N N N 0 6.513 1.631 1.044
22 C16 C C20 N N N 0 7.203 0.067 -0.778
23 N18 N N2 N N N 0 9.568 -0.343 -1.263
24 C19 C C21 N N N 0 9.436 -0.677 -2.704
25 O23 O O2 N N N 0 3.576 2.823 3.328
26 N24 N N3 N N N 0 -0.811 1.532 -0.308
27 C25 C C22 N Y N 0 -1.906 2.403 -0.277
28 C27 C C23 N Y N 0 -3.261 3.994 0.899
29 C29 C C24 N Y N 0 -3.801 3.394 -1.364
30 C30 C C25 N Y N 0 -2.72 2.535 -1.395
31 O31 O O3 N N N 0 -5.135 4.974 -0.19
32 C32 C C26 N N N 0 -5.926 5.064 -1.377
33 N33 N N4 N N N 0 -6.846 3.92 -1.44
34 C34 C C27 N N N 0 -8.112 4.216 -0.722
35 C35 C C28 N N N 0 -9.106 3.188 -1.32
36 C36 C C29 N N N 0 -8.689 3.129 -2.807
37 C37 C C30 N N N 0 -7.233 3.628 -2.837
38 N38 N N5 N N N 0 -2.125 -1.068 0.811
39 C39 C C31 N N N 0 -1.061 -1.444 -0.13
40 C40 C C32 N N N 0 -0.843 -2.959 -0.047
41 C41 C C33 N N N 0 -2.175 -3.675 -0.285
42 C42 C C34 N N N 0 -3.174 -3.271 0.801
43 C43 C C35 N N N 0 -3.417 -1.765 0.732
44 C44 C C36 N N N 0 -1.954 -5.188 -0.238
45 C45 C C37 N N N 0 -3.257 -5.905 -0.598
46 N46 N N6 N N N 0 -3.046 -7.358 -0.553
47 C50 C C41 N N N 0 -4.204 -8.08 -1.123
48 C47 C C38 N N N 0 -2.921 -7.834 0.848
49 C48 C C39 N N N 0 -3.236 -9.347 0.738
50 C49 C C40 N N N 0 -4.355 -9.391 -0.328
51 H1 H H1 N N N 0 6.25 1.978 -1.066
52 H2 H H2 N N N 0 5.663 3.598 0.793
53 H3 H H3 N N N 0 5.681 3.013 2.477
54 H4 H H4 N N N 0 8.593 1.485 -1.614
55 H5 H H5 N N N 0 8.877 1.1 0.1
56 H6 H H6 N N N 0 11.083 -1.012 -4.088
57 H7 H H7 N N N 0 10.734 -2.399 -3.013
58 H8 H H8 N N N 0 12.228 -1.579 -1.469
59 H9 H H9 N N N 0 12.578 -0.192 -2.545
60 H10 H H10 N N N 0 11.298 0.075 -0.098
61 H11 H H11 N N N 0 11.028 1.193 -1.469
62 H12 H H12 N N N 0 -1.55 3.031 1.741
63 H13 H H13 N N N 0 1.592 2.504 0.196
64 H14 H H14 N N N 0 1.992 0.687 4.057
65 H15 H H15 N N N 0 -0.231 -0.326 3.823
66 H16 H H16 N N N 0 2.774 1.199 0.054
67 H17 H H17 N N N 0 3.769 2.416 -0.785
68 H18 H H18 N N N 0 4.562 0.18 -1.401
69 H19 H H19 N N N 0 4.715 -0.271 0.315
70 H20 H H20 N N N 0 6.431 0.8 1.745
71 H21 H H21 N N N 0 7.527 2.03 1.07
72 H22 H H22 N N N 0 7.208 -0.729 -0.034
73 H23 H H23 N N N 0 6.924 -0.344 -1.748
74 H25 H H25 N N N 0 9.263 0.226 -3.289
75 H26 H H26 N N N 0 8.626 -1.391 -2.856
76 H27 H H27 N N N 0 -0.571 1.083 -1.133
77 H28 H H28 N N N 0 -3.477 4.561 1.793
78 H29 H H29 N N N 0 -4.437 3.493 -2.232
79 H30 H H30 N N N 0 -2.508 1.965 -2.288
80 H31 H H31 N N N 0 -6.499 5.991 -1.363
81 H32 H H32 N N N 0 -5.273 5.054 -2.25
82 H34 H H34 N N N 0 -7.993 4.057 0.35
83 H35 H H35 N N N 0 -8.442 5.234 -0.927
84 H36 H H36 N N N 0 -8.985 2.214 -0.846
85 H37 H H37 N N N 0 -10.132 3.542 -1.22
86 H38 H H38 N N N 0 -8.746 2.105 -3.175
87 H39 H H39 N N N 0 -9.325 3.782 -3.405
88 H40 H H40 N N N 0 -7.163 4.534 -3.439
89 H41 H H41 N N N 0 -6.584 2.855 -3.248
90 H42 H H42 N N N 0 -1.356 -1.172 -1.143
91 H46 H H46 N N N 0 -2.568 -3.396 -1.263
92 H43 H H43 N N N 0 -0.139 -0.928 0.136
93 H44 H H44 N N N 0 -0.125 -3.265 -0.808
94 H45 H H45 N N N 0 -0.462 -3.218 0.94
95 H47 H H47 N N N 0 -4.115 -3.8 0.644
96 H48 H H48 N N N 0 -2.771 -3.528 1.78
97 H49 H H49 N N N 0 -4.048 -1.459 1.566
98 H50 H H50 N N N 0 -3.908 -1.519 -0.21
99 H51 H H51 N N N 0 -1.178 -5.465 -0.951
100 H52 H H52 N N N 0 -1.646 -5.48 0.766
101 H53 H H53 N N N 0 -4.034 -5.628 0.115
102 H54 H H54 N N N 0 -3.566 -5.614 -1.602
103 H56 H H56 N N N 0 -1.908 -7.678 1.219
104 H57 H H57 N N N 0 -3.648 -7.336 1.49
105 H58 H H58 N N N 0 -2.36 -9.9 0.4
106 H59 H H59 N N N 0 -3.596 -9.737 1.69
107 H60 H H60 N N N 0 -4.218 -10.249 -0.986
108 H61 H H61 N N N 0 -5.333 -9.432 0.151
109 H62 H H62 N N N 0 -5.106 -7.477 -1.018
110 H63 H H63 N N N 0 -4.023 -8.302 -2.174



6PD : Chemical Bonds

Total Number of Bonds: 116
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O01 C02 O C doub 1.22 N N
2 C39 N38 C N sing 1.47 N N
3 C39 C40 C C sing 1.53 N N
4 C02 N38 C N sing 1.35 N N
5 C02 C03 C C sing 1.48 N N
6 C08 C07 C C doub 1.38 N Y
7 C08 C03 C C sing 1.4 N Y
8 N38 C43 N C sing 1.47 N N
9 C07 C06 C C sing 1.4 N Y
10 C40 C41 C C sing 1.53 N N
11 C03 C04 C C doub 1.4 N Y
12 C43 C42 C C sing 1.53 N N
13 C06 C05 C C doub 1.39 N Y
14 C06 C09 C C sing 1.48 N N
15 C04 C05 C C sing 1.39 N Y
16 C04 N24 C N sing 1.39 N N
17 C41 C42 C C sing 1.53 N N
18 C41 C44 C C sing 1.53 N N
19 C15 N10 C N sing 1.47 N N
20 C15 C14 C C sing 1.53 N N
21 C44 C45 C C sing 1.53 N N
22 C09 N10 C N sing 1.35 N N
23 C09 O23 C O doub 1.22 N N
24 N10 C11 N C sing 1.47 N N
25 N24 C25 N C sing 1.4 N N
26 C47 C48 C C sing 1.55 N N
27 C47 N46 C N sing 1.48 N N
28 C14 C13 C C sing 1.53 N N
29 C11 C12 C C sing 1.53 N N
30 C48 C49 C C sing 1.55 N N
31 C45 N46 C N sing 1.47 N N
32 C25 C30 C C doub 1.39 N Y
33 C25 C26 C C sing 1.39 N Y
34 C13 C12 C C sing 1.53 N N
35 C13 C16 C C sing 1.53 N N
36 N46 C50 N C sing 1.48 N N
37 C30 C29 C C sing 1.38 N Y
38 C19 C20 C C sing 1.54 N N
39 C19 N18 C N sing 1.49 N N
40 C20 C21 C C sing 1.54 N N
41 C26 C27 C C doub 1.38 N Y
42 C49 C50 C C sing 1.54 N N
43 C16 C17 C C sing 1.53 N N
44 N18 C17 N C sing 1.47 N N
45 N18 C22 N C sing 1.49 N N
46 C29 C28 C C doub 1.39 N Y
47 C34 C35 C C sing 1.55 N N
48 C34 N33 C N sing 1.49 N N
49 C35 C36 C C sing 1.55 N N
50 C21 C22 C C sing 1.54 N N
51 C27 C28 C C sing 1.39 N Y
52 C28 O31 C O sing 1.36 N N
53 C36 C37 C C sing 1.54 N N
54 N33 C32 N C sing 1.47 N N
55 N33 C37 N C sing 1.48 N N
56 C32 O31 C O sing 1.43 N N
57 C13 H1 C H sing 1.09 N N
58 C15 H2 C H sing 1.09 N N
59 C15 H3 C H sing 1.09 N N
60 C17 H4 C H sing 1.09 N N
61 C17 H5 C H sing 1.09 N N
62 C20 H6 C H sing 1.09 N N
63 C20 H7 C H sing 1.09 N N
64 C21 H8 C H sing 1.09 N N
65 C21 H9 C H sing 1.09 N N
66 C22 H10 C H sing 1.09 N N
67 C22 H11 C H sing 1.09 N N
68 C26 H12 C H sing 1.08 N N
69 C05 H13 C H sing 1.08 N N
70 C07 H14 C H sing 1.08 N N
71 C08 H15 C H sing 1.08 N N
72 C11 H16 C H sing 1.09 N N
73 C11 H17 C H sing 1.09 N N
74 C12 H18 C H sing 1.09 N N
75 C12 H19 C H sing 1.09 N N
76 C14 H20 C H sing 1.09 N N
77 C14 H21 C H sing 1.09 N N
78 C16 H22 C H sing 1.09 N N
79 C16 H23 C H sing 1.09 N N
80 C19 H25 C H sing 1.09 N N
81 C19 H26 C H sing 1.09 N N
82 N24 H27 N H sing 0.97 N N
83 C27 H28 C H sing 1.08 N N
84 C29 H29 C H sing 1.08 N N
85 C30 H30 C H sing 1.08 N N
86 C32 H31 C H sing 1.09 N N
87 C32 H32 C H sing 1.09 N N
88 C34 H34 C H sing 1.09 N N
89 C34 H35 C H sing 1.09 N N
90 C35 H36 C H sing 1.09 N N
91 C35 H37 C H sing 1.09 N N
92 C36 H38 C H sing 1.09 N N
93 C36 H39 C H sing 1.09 N N
94 C37 H40 C H sing 1.09 N N
95 C37 H41 C H sing 1.09 N N
96 C39 H42 C H sing 1.09 N N
97 C39 H43 C H sing 1.09 N N
98 C40 H44 C H sing 1.09 N N
99 C40 H45 C H sing 1.09 N N
100 C41 H46 C H sing 1.09 N N
101 C42 H47 C H sing 1.09 N N
102 C42 H48 C H sing 1.09 N N
103 C43 H49 C H sing 1.09 N N
104 C43 H50 C H sing 1.09 N N
105 C44 H51 C H sing 1.09 N N
106 C44 H52 C H sing 1.09 N N
107 C45 H53 C H sing 1.09 N N
108 C45 H54 C H sing 1.09 N N
109 C47 H56 C H sing 1.09 N N
110 C47 H57 C H sing 1.09 N N
111 C48 H58 C H sing 1.09 N N
112 C48 H59 C H sing 1.09 N N
113 C49 H60 C H sing 1.09 N N
114 C49 H61 C H sing 1.09 N N
115 C50 H62 C H sing 1.09 N N
116 C50 H63 C H sing 1.09 N N



6PD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
6PD 5jsj Open in New Window Bound ligand 2 1