Chemical Components in the PDB

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JDG : Summary

Code

JDG

One-letter code

X

Molecule name

2-cyclohexyl-7-methoxy-N-[1-(propan-2-yl)piperidin-4-yl]-8-[3-(pyrrolidin-1-yl)propoxy]-3H-1,4-benzodiazepin-5-amine

Systematic names

ProgramVersionName
ACDLabs 12.01 2-cyclohexyl-7-methoxy-N-[1-(propan-2-yl)piperidin-4-yl]-8-[3-(pyrrolidin-1-yl)propoxy]-3H-1,4-benzodiazepin-5-amine
OpenEye OEToolkits 2.0.6 2-cyclohexyl-7-methoxy-~{N}-(1-propan-2-ylpiperidin-4-yl)-8-(3-pyrrolidin-1-ylpropoxy)-3~{H}-1,4-benzodiazepin-5-amine

Formula

C31 H49 N5 O2

Formal charge

0

Molecular weight

523.753 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 C1N(CCC1)CCCOc5c(cc2c(N=C(CN=C2NC3CCN(CC3)C(C)C)C4CCCCC4)c5)OC
SMILES CACTVS 3.385 COc1cc2C(=NCC(=Nc2cc1OCCCN3CCCC3)C4CCCCC4)NC5CCN(CC5)C(C)C
SMILES OpenEye OEToolkits 2.0.6 CC(C)N1CCC(CC1)NC2=NCC(=Nc3c2cc(c(c3)OCCCN4CCCC4)OC)C5CCCCC5
Canonical SMILES CACTVS 3.385 COc1cc2C(=NCC(=Nc2cc1OCCCN3CCCC3)C4CCCCC4)NC5CCN(CC5)C(C)C
Canonical SMILES OpenEye OEToolkits 2.0.6 CC(C)N1CCC(CC1)NC2=NCC(=Nc3c2cc(c(c3)OCCCN4CCCC4)OC)C5CCCCC5

IUPAC InChI

InChI=1S/C31H49N5O2/c1-23(2)36-17-12-25(13-18-36)33-31-26-20-29(37-3)30(38-19-9-16-35-14-7-8-15-35)21-27(26)34-28(22-32-31)24-10-5-4-6-11-24/h20-21,23-25H,4-19,22H2,1-3H3,(H,32,33)

IUPAC InChI key

CEYUGMZUIYBLTQ-UHFFFAOYSA-N
JDG

wwPDB Information

Atom count

87 (38 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2018-08-31

Last modified at

2019-02-22

Status

Released

Obsoleted

Not Assigned



JDG : Atoms of Molecule

Total Number of Atoms: 87
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N N N 0 9.311 0.148 0.353
2 C13 C C2 N N N 0 8.522 -1.601 -1.084
3 C15 C C3 N Y N 0 0.535 0.392 0.269
4 C17 C C4 N N N 0 -1.913 -0.21 0.372
5 C20 C C5 N N N 0 -4.863 -1.241 -1.62
6 C21 C C6 N N N 0 -6.368 -0.967 -1.587
7 C24 C C7 N N N 0 -8.975 -2.063 -1.711
8 C26 C C8 N N N 0 -6.389 -1.053 0.835
9 C01 C C9 N N N 0 0.385 -4.568 0.478
10 C03 C C10 N Y N 0 1.168 -2.325 0.375
11 C04 C C11 N Y N 0 2.185 -1.373 0.313
12 C06 C C12 N N N 0 4.475 -0.739 0.243
13 C07 C C13 N N N 0 5.868 -1.371 0.245
14 C08 C C14 N N N 0 6.928 -0.27 0.176
15 C11 C C15 N N N 0 10.27 0.033 -0.851
16 C12 C C16 N N N 0 10.039 -1.42 -1.343
17 C14 C C17 N Y N 0 1.872 -0.029 0.261
18 C16 C C18 N Y N 0 -0.486 -0.563 0.34
19 C19 C C19 N N N 0 -4.22 -0.686 -0.347
20 C23 C C20 N N N 0 -8.421 -1.48 -0.41
21 C25 C C21 N N N 0 -9.004 -2.243 0.781
22 C27 C C22 N N N 0 -4.884 -1.33 0.874
23 C29 C C23 N N N 0 -1.531 1.684 1.802
24 C30 C C24 N N N 0 -0.582 2.367 0.858
25 C31 C C25 N N N 0 -0.68 3.861 0.686
26 C32 C C26 N N N 0 -2.025 4.214 0.049
27 C33 C C27 N N N 0 -2.124 5.731 -0.125
28 C34 C C28 N N N 0 -0.989 6.216 -1.029
29 C35 C C29 N N N 0 0.356 5.863 -0.392
30 C36 C C30 N N N 0 0.456 4.346 -0.218
31 C38 C C31 N Y N 0 -0.152 -1.925 0.388
32 N09 N N1 N N N 0 8.266 -0.877 0.179
33 N18 N N2 N N N 0 -2.788 -0.996 -0.346
34 N22 N N3 N N N 0 -6.957 -1.604 -0.402
35 N28 N N4 N N N 0 -2.398 0.789 1.028
36 N37 N N5 N N N 0 0.302 1.732 0.199
37 O02 O O1 N N N 0 1.477 -3.648 0.419
38 O05 O O2 N N N 0 3.485 -1.768 0.307
39 H1 H H1 N N N 0 9.856 -0.031 1.28
40 H2 H H2 N N N 0 8.858 1.14 0.376
41 H3 H H3 N N N 0 7.944 -1.162 -1.897
42 H4 H H4 N N N 0 8.279 -2.658 -0.974
43 H5 H H5 N N N 0 -4.69 -2.316 -1.677
44 H11 H H11 N N N 0 -8.56 -1.519 -2.559
45 H6 H H6 N N N 0 -4.424 -0.755 -2.491
46 H7 H H7 N N N 0 -6.541 0.108 -1.544
47 H8 H H8 N N N 0 -6.832 -1.374 -2.486
48 H9 H H9 N N N 0 -8.7 -3.115 -1.783
49 H10 H H10 N N N 0 -10.061 -1.971 -1.716
50 H12 H H12 N N N 0 -6.866 -1.522 1.695
51 H13 H H13 N N N 0 -6.561 0.023 0.866
52 H17 H H17 N N N 0 4.373 -0.081 1.106
53 H14 H H14 N N N 0 0.77 -5.588 0.509
54 H15 H H15 N N N 0 -0.205 -4.375 1.374
55 H16 H H16 N N N 0 -0.243 -4.444 -0.404
56 H18 H H18 N N N 0 4.34 -0.162 -0.672
57 H19 H H19 N N N 0 6.003 -1.949 1.16
58 H20 H H20 N N N 0 5.971 -2.029 -0.618
59 H21 H H21 N N N 0 6.793 0.308 -0.738
60 H22 H H22 N N N 0 6.826 0.387 1.04
61 H23 H H23 N N N 0 10.002 0.75 -1.627
62 H24 H H24 N N N 0 11.304 0.173 -0.535
63 H25 H H25 N N N 0 10.622 -2.129 -0.756
64 H26 H H26 N N N 0 10.267 -1.513 -2.405
65 H27 H H27 N N N 0 2.663 0.704 0.213
66 H28 H H28 N N N 0 -4.358 0.395 -0.31
67 H29 H H29 N N N 0 -8.696 -0.428 -0.337
68 H30 H H30 N N N 0 -8.728 -3.295 0.708
69 H31 H H31 N N N 0 -8.609 -1.828 1.708
70 H32 H H32 N N N 0 -10.09 -2.151 0.775
71 H33 H H33 N N N 0 -4.459 -0.907 1.784
72 H34 H H34 N N N 0 -4.711 -2.406 0.857
73 H35 H H35 N N N 0 -0.967 1.107 2.533
74 H36 H H36 N N N 0 -2.137 2.431 2.314
75 H38 H H38 N N N 0 -0.601 4.345 1.66
76 H39 H H39 N N N 0 -2.104 3.731 -0.925
77 H40 H H40 N N N 0 -2.834 3.869 0.692
78 H41 H H41 N N N 0 -3.083 5.983 -0.58
79 H42 H H42 N N N 0 -2.046 6.215 0.848
80 H43 H H43 N N N 0 -1.068 5.733 -2.003
81 H44 H H44 N N N 0 -1.06 7.297 -1.153
82 H45 H H45 N N N 0 1.165 6.209 -1.036
83 H46 H H46 N N N 0 0.435 6.346 0.582
84 H47 H H47 N N N 0 1.414 4.095 0.236
85 H48 H H48 N N N 0 0.377 3.863 -1.191
86 H49 H H49 N N N 0 -0.936 -2.666 0.437
87 H37 H H37 N N N 0 -2.456 -1.755 -0.85



JDG : Chemical Bonds

Total Number of Bonds: 91
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C24 C23 C C sing 1.53 N N
2 C11 C10 C C sing 1.54 N N
3 C11 C12 C C sing 1.55 N N
4 C23 N22 C N sing 1.47 N N
5 C23 C25 C C sing 1.53 N N
6 C10 N09 C N sing 1.47 N N
7 N22 C26 N C sing 1.47 N N
8 N22 C21 N C sing 1.47 N N
9 C01 O02 C O sing 1.43 N N
10 C12 C13 C C sing 1.55 N N
11 C26 C27 C C sing 1.53 N N
12 C21 C20 C C sing 1.53 N N
13 C27 C19 C C sing 1.53 N N
14 C20 C19 C C sing 1.53 N N
15 O02 C03 O C sing 1.36 N N
16 N09 C13 N C sing 1.48 N N
17 N09 C08 N C sing 1.47 N N
18 C19 N18 C N sing 1.47 N N
19 C08 C07 C C sing 1.53 N N
20 N18 C17 N C sing 1.38 N N
21 C03 C38 C C sing 1.38 N Y
22 C03 C04 C C doub 1.39 N Y
23 C38 C16 C C doub 1.4 N Y
24 O05 C04 O C sing 1.36 N N
25 O05 C06 O C sing 1.43 N N
26 C04 C14 C C sing 1.38 N Y
27 C17 C16 C C sing 1.47 N N
28 C17 N28 C N doub 1.29 N N
29 C16 C15 C C sing 1.4 N Y
30 C07 C06 C C sing 1.53 N N
31 C14 C15 C C doub 1.4 N Y
32 C15 N37 C N sing 1.36 N N
33 N28 C29 N C sing 1.47 N N
34 C29 C30 C C sing 1.5 N N
35 N37 C30 N C doub 1.27 N N
36 C30 C31 C C sing 1.51 N N
37 C32 C31 C C sing 1.53 N N
38 C32 C33 C C sing 1.53 N N
39 C31 C36 C C sing 1.53 N N
40 C33 C34 C C sing 1.53 N N
41 C36 C35 C C sing 1.53 N N
42 C34 C35 C C sing 1.53 N N
43 C10 H1 C H sing 1.09 N N
44 C10 H2 C H sing 1.09 N N
45 C13 H3 C H sing 1.09 N N
46 C13 H4 C H sing 1.09 N N
47 C20 H5 C H sing 1.09 N N
48 C20 H6 C H sing 1.09 N N
49 C21 H7 C H sing 1.09 N N
50 C21 H8 C H sing 1.09 N N
51 C24 H9 C H sing 1.09 N N
52 C24 H10 C H sing 1.09 N N
53 C24 H11 C H sing 1.09 N N
54 C26 H12 C H sing 1.09 N N
55 C26 H13 C H sing 1.09 N N
56 C01 H14 C H sing 1.09 N N
57 C01 H15 C H sing 1.09 N N
58 C01 H16 C H sing 1.09 N N
59 C06 H17 C H sing 1.09 N N
60 C06 H18 C H sing 1.09 N N
61 C07 H19 C H sing 1.09 N N
62 C07 H20 C H sing 1.09 N N
63 C08 H21 C H sing 1.09 N N
64 C08 H22 C H sing 1.09 N N
65 C11 H23 C H sing 1.09 N N
66 C11 H24 C H sing 1.09 N N
67 C12 H25 C H sing 1.09 N N
68 C12 H26 C H sing 1.09 N N
69 C14 H27 C H sing 1.08 N N
70 C19 H28 C H sing 1.09 N N
71 C23 H29 C H sing 1.09 N N
72 C25 H30 C H sing 1.09 N N
73 C25 H31 C H sing 1.09 N N
74 C25 H32 C H sing 1.09 N N
75 C27 H33 C H sing 1.09 N N
76 C27 H34 C H sing 1.09 N N
77 C29 H35 C H sing 1.09 N N
78 C29 H36 C H sing 1.09 N N
79 C31 H38 C H sing 1.09 N N
80 C32 H39 C H sing 1.09 N N
81 C32 H40 C H sing 1.09 N N
82 C33 H41 C H sing 1.09 N N
83 C33 H42 C H sing 1.09 N N
84 C34 H43 C H sing 1.09 N N
85 C34 H44 C H sing 1.09 N N
86 C35 H45 C H sing 1.09 N N
87 C35 H46 C H sing 1.09 N N
88 C36 H47 C H sing 1.09 N N
89 C36 H48 C H sing 1.09 N N
90 C38 H49 C H sing 1.08 N N
91 N18 H37 N H sing 0.97 N N



JDG : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
JDG 6mbo Open in New Window Bound ligand 4 1
JDG 6mbp Open in New Window Bound ligand 2 1