Chemical Components in the PDB

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DJ8 : Summary

Code

DJ8

One-letter code

X

Molecule name

1-[(4-chloranyl-2-methyl-phenyl)methyl]-3-(7,10-dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.1^{2,6}.0^{17,20}]docosa-1(20),2(22),3,5,14(21),15,18-heptaen-5-yl)urea

Systematic names

ProgramVersionName
OpenEye OEToolkits 3.1.0.0 1-[(4-chloranyl-2-methyl-phenyl)methyl]-3-(7,10-dioxa-13,17,18,21-tetrazatetracyclo[12.5.2.1^{2,6}.0^{17,20}]docosa-1(20),2(22),3,5,14(21),15,18-heptaen-5-yl)urea

Formula

C25 H25 Cl N6 O3

Formal charge

0

Molecular weight

492.957 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 Cc1cc(Cl)ccc1CNC(=O)Nc2ccc3cc2OCCOCCNc4ccn5ncc3c5n4
SMILES OpenEye OEToolkits 2.0.7 Cc1cc(ccc1CNC(=O)Nc2ccc-3cc2OCCOCCNc4ccn5c(c3cn5)n4)Cl
Canonical SMILES CACTVS 3.385 Cc1cc(Cl)ccc1CNC(=O)Nc2ccc3cc2OCCOCCNc4ccn5ncc3c5n4
Canonical SMILES OpenEye OEToolkits 2.0.7 Cc1cc(ccc1CNC(=O)Nc2ccc-3cc2OCCOCCNc4ccn5c(c3cn5)n4)Cl

IUPAC InChI

InChI=1S/C25H25ClN6O3/c1-16-12-19(26)4-2-18(16)14-28-25(33)30-21-5-3-17-13-22(21)35-11-10-34-9-7-27-23-6-8-32-24(31-23)20(17)15-29-32/h2-6,8,12-13,15H,7,9-11,14H2,1H3,(H,27,31)(H2,28,30,33)

IUPAC InChI key

SMEVONJPJBGLLE-UHFFFAOYSA-N
DJ8

wwPDB Information

Atom count

60 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-12-15

Last modified at

2022-08-22

Status

Released

Obsoleted

Not Assigned



DJ8 : 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 N1 N N1 N N N 0 -1.314 0.109 -0.271
2 C7 C C1 N N N 0 -4.649 1.471 0.463
3 C8 C C2 N N N 0 -2.294 0.935 0.148
4 N2 N N2 N N N 0 6.981 -2.053 -0.111
5 C9 C C3 N Y N 0 0.023 0.533 -0.234
6 O1 O O1 N N N 0 0.734 -1.731 -0.127
7 C1 C C4 N Y N 0 -6.483 -0.127 1.052
8 C5 C C5 N Y N 0 -6.726 1.221 -0.912
9 C6 C C6 N Y N 0 -5.99 0.837 0.194
10 N3 N N3 N Y N 0 6.283 1.987 0.047
11 C4 C C7 N Y N 0 -7.955 0.641 -1.159
12 C3 C C8 N Y N 0 -8.447 -0.329 -0.304
13 C2 C C9 N Y N 0 -7.71 -0.713 0.802
14 N4 N N4 N Y N 0 5.745 3.279 0.047
15 O O O2 N N N 0 -2.013 2.005 0.652
16 N N N5 N N N 0 -3.585 0.574 0.008
17 CL CL CL1 N N N 0 -9.991 -1.059 -0.614
18 C C C10 N N N 0 -5.68 -0.545 2.257
19 C14 C C11 N Y N 0 1.048 -0.41 -0.157
20 C13 C C12 N Y N 0 2.365 0.008 -0.108
21 C15 C C13 N N N 0 1.683 -2.646 -0.679
22 C16 C C14 N N N 0 2.4 -3.367 0.465
23 O2 O O3 N N N 0 3.707 -3.755 0.057
24 C17 C C15 N N N 0 4.748 -2.864 0.463
25 C18 C C16 N N N 0 5.858 -2.894 -0.589
26 C19 C C17 N Y N 0 6.724 -0.68 -0.043
27 N5 N N6 N Y N 0 5.492 -0.22 -0.105
28 C24 C C18 N Y N 0 5.245 1.095 -0.054
29 C21 C C19 N Y N 0 7.572 1.537 0.13
30 C20 C C20 N Y N 0 7.811 0.208 0.089
31 C23 C C21 N Y N 0 4.068 1.849 -0.081
32 C22 C C22 N Y N 0 4.442 3.202 -0.024
33 C12 C C23 N Y N 0 2.667 1.366 -0.143
34 C11 C C24 N Y N 0 1.633 2.305 -0.233
35 C10 C C25 N Y N 0 0.321 1.886 -0.276
36 H1 H H1 N N N 0 -1.533 -0.778 -0.594
37 H2 H H2 N N N 0 -4.581 2.418 -0.073
38 H3 H H3 N N N 0 -4.541 1.651 1.533
39 H4 H H4 N N N 0 7.837 -2.431 0.143
40 H5 H H5 N N N 0 -6.34 1.975 -1.582
41 H6 H H6 N N N 0 -8.531 0.941 -2.023
42 H7 H H7 N N N 0 -8.093 -1.47 1.47
43 H8 H H8 N N N 0 -3.809 -0.28 -0.395
44 H9 H H9 N N N 0 -5.945 0.086 3.106
45 H10 H H10 N N N 0 -5.898 -1.586 2.496
46 H11 H H11 N N N 0 -4.617 -0.436 2.041
47 H12 H H12 N N N 0 3.16 -0.72 -0.042
48 H13 H H13 N N N 0 1.167 -3.375 -1.304
49 H14 H H14 N N N 0 2.409 -2.099 -1.281
50 H15 H H15 N N N 0 2.48 -2.698 1.322
51 H16 H H16 N N N 0 1.832 -4.253 0.748
52 H17 H H17 N N N 0 4.352 -1.852 0.547
53 H18 H H18 N N N 0 5.148 -3.184 1.425
54 H19 H H19 N N N 0 5.479 -2.499 -1.532
55 H20 H H20 N N N 0 6.201 -3.919 -0.73
56 H21 H H21 N N N 0 8.389 2.237 0.226
57 H22 H H22 N N N 0 8.821 -0.169 0.156
58 H23 H H23 N N N 0 3.763 4.042 -0.038
59 H25 H H25 N N N 0 -0.475 2.613 -0.341
60 H24 H H24 N N N 0 1.864 3.359 -0.27



DJ8 : 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 C4 C5 C C doub 1.38 N Y
2 C4 C3 C C sing 1.38 N Y
3 CL C3 CL C sing 1.74 N N
4 O2 C16 O C sing 1.42 N N
5 O2 C17 O C sing 1.43 N N
6 C5 C6 C C sing 1.38 N Y
7 C16 C15 C C sing 1.53 N N
8 C3 C2 C C doub 1.38 N Y
9 C15 O1 C O sing 1.43 N N
10 C17 C18 C C sing 1.53 N N
11 C18 N2 C N sing 1.48 N N
12 C6 C7 C C sing 1.51 N N
13 C6 C1 C C doub 1.38 N Y
14 O1 C14 O C sing 1.36 N N
15 N C7 N C sing 1.46 N N
16 N C8 N C sing 1.35 N N
17 C2 C1 C C sing 1.38 N Y
18 C1 C C C sing 1.51 N N
19 N1 C8 N C sing 1.35 N N
20 N1 C9 N C sing 1.4 N N
21 N2 C19 N C sing 1.4 N N
22 C14 C9 C C doub 1.39 N Y
23 C14 C13 C C sing 1.38 N Y
24 C8 O C O doub 1.22 N N
25 C9 C10 C C sing 1.39 N Y
26 C13 C12 C C doub 1.39 N Y
27 C19 N5 C N doub 1.32 N Y
28 C19 C20 C C sing 1.41 N Y
29 N5 C24 N C sing 1.34 N Y
30 C10 C11 C C doub 1.38 N Y
31 C12 C11 C C sing 1.4 N Y
32 C12 C23 C C sing 1.48 N N
33 C20 C21 C C doub 1.35 N Y
34 C24 C23 C C doub 1.4 N Y
35 C24 N3 C N sing 1.37 N Y
36 C23 C22 C C sing 1.4 N Y
37 C21 N3 C N sing 1.37 N Y
38 N3 N4 N N sing 1.4 N Y
39 C22 N4 C N doub 1.31 N Y
40 N1 H1 N H sing 0.97 N N
41 C7 H2 C H sing 1.09 N N
42 C7 H3 C H sing 1.09 N N
43 N2 H4 N H sing 0.97 N N
44 C5 H5 C H sing 1.08 N N
45 C4 H6 C H sing 1.08 N N
46 C2 H7 C H sing 1.08 N N
47 N H8 N H sing 0.97 N N
48 C H9 C H sing 1.09 N N
49 C H10 C H sing 1.09 N N
50 C H11 C H sing 1.09 N N
51 C13 H12 C H sing 1.08 N N
52 C15 H13 C H sing 1.09 N N
53 C15 H14 C H sing 1.09 N N
54 C16 H15 C H sing 1.09 N N
55 C16 H16 C H sing 1.09 N N
56 C17 H17 C H sing 1.09 N N
57 C17 H18 C H sing 1.09 N N
58 C18 H19 C H sing 1.09 N N
59 C18 H20 C H sing 1.09 N N
60 C21 H21 C H sing 1.08 N N
61 C20 H22 C H sing 1.08 N N
62 C22 H23 C H sing 1.08 N N
63 C11 H24 C H sing 1.08 N N
64 C10 H25 C H sing 1.08 N N



DJ8 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
DJ8 7qgp Open in New Window Bound ligand 1 1