Chemical Components in the PDB

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XJ4 : Summary

Code

XJ4

One-letter code

X

Molecule name

N'-[[3-[4-(3,5-dimethyl-1,2-oxazol-4-yl)-5-methyl-6-phenylazanyl-pyrimidin-2-yl]phenyl]methyl]-N-methyl-ethane-1,2-diamine

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 ~{N}'-[[3-[4-(3,5-dimethyl-1,2-oxazol-4-yl)-5-methyl-6-phenylazanyl-pyrimidin-2-yl]phenyl]methyl]-~{N}-methyl-ethane-1,2-diamine

Formula

C26 H30 N6 O

Formal charge

0

Molecular weight

442.556 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CNCCNCc1cccc(c1)c2nc(Nc3ccccc3)c(C)c(n2)c4c(C)onc4C
SMILES OpenEye OEToolkits 2.0.6 Cc1c(nc(nc1Nc2ccccc2)c3cccc(c3)CNCCNC)c4c(noc4C)C
Canonical SMILES CACTVS 3.385 CNCCNCc1cccc(c1)c2nc(Nc3ccccc3)c(C)c(n2)c4c(C)onc4C
Canonical SMILES OpenEye OEToolkits 2.0.6 Cc1c(nc(nc1Nc2ccccc2)c3cccc(c3)CNCCNC)c4c(noc4C)C

IUPAC InChI

InChI=1S/C26H30N6O/c1-17-24(23-18(2)32-33-19(23)3)30-26(31-25(17)29-22-11-6-5-7-12-22)21-10-8-9-20(15-21)16-28-14-13-27-4/h5-12,15,27-28H,13-14,16H2,1-4H3,(H,29,30,31)

IUPAC InChI key

DVIUIRPCVXVFSX-UHFFFAOYSA-N
XJ4

wwPDB Information

Atom count

63 (33 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-01-10

Last modified at

2021-11-19

Status

Released

Obsoleted

Not Assigned



XJ4 : Atoms of Molecule

Total Number of Atoms: 63
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 8.76 0.489 -2.382
2 C3 C C2 N N N 0 6.671 1.022 -1.281
3 C4 C C3 N N N 0 5.971 1.092 0.078
4 C6 C C4 N N N 0 3.881 1.625 1.179
5 C7 C C5 N Y N 0 2.467 2.093 0.949
6 C8 C C6 N Y N 0 1.466 1.172 0.719
7 C9 C C7 N Y N 0 0.158 1.607 0.507
8 C10 C C8 N Y N 0 -0.923 0.622 0.259
9 C12 C C9 N Y N 0 -1.569 -1.584 0.031
10 C14 C C10 N Y N 0 0.04 -3.35 0.358
11 C15 C C11 N Y N 0 0.769 -2.649 1.31
12 C16 C C12 N Y N 0 2.043 -3.063 1.646
13 C17 C C13 N Y N 0 2.593 -4.174 1.035
14 C18 C C14 N Y N 0 1.871 -4.875 0.086
15 C19 C C15 N Y N 0 0.594 -4.47 -0.249
16 C20 C C16 N Y N 0 -2.881 -1.167 -0.189
17 C21 C C17 N N N 0 -3.978 -2.169 -0.44
18 C22 C C18 N Y N 0 -3.154 0.201 -0.165
19 C23 C C19 N Y N 0 -4.533 0.695 -0.393
20 C24 C C20 N Y N 0 -5.347 1.362 0.481
21 C25 C C21 N N N 0 -5.023 1.753 1.9
22 C28 C C22 N Y N 0 -5.32 0.595 -1.575
23 C29 C C23 N N N 0 -4.919 -0.049 -2.877
24 C31 C C24 N Y N 0 -0.129 2.97 0.528
25 C32 C C25 N Y N 0 0.881 3.882 0.759
26 C33 C C26 N Y N 0 2.175 3.445 0.975
27 N2 N N1 N N N 0 8.056 0.568 -1.096
28 N5 N N2 N N N 0 4.586 1.546 -0.108
29 N11 N N3 N Y N 0 -0.627 -0.671 0.249
30 N13 N N4 N N N 0 -1.25 -2.934 0.017
31 N27 N N5 N Y N 0 -6.455 1.168 -1.306
32 N30 N N6 N Y N 0 -2.158 1.056 0.06
33 O26 O O1 N Y N 0 -6.489 1.597 -0.176
34 H1 H H1 N N N 0 8.246 -0.215 -3.036
35 H2 H H2 N N N 0 8.775 1.474 -2.849
36 H3 H H3 N N N 0 9.783 0.151 -2.216
37 H4 H H4 N N N 0 6.142 0.321 -1.927
38 H5 H H5 N N N 0 6.671 2.011 -1.741
39 H6 H H6 N N N 0 5.97 0.104 0.537
40 H7 H H7 N N N 0 6.5 1.793 0.723
41 H8 H H8 N N N 0 4.396 2.33 1.832
42 H9 H H9 N N N 0 3.866 0.64 1.646
43 H10 H H10 N N N 0 1.694 0.117 0.703
44 H14 H H14 N N N 0 2.304 -5.742 -0.39
45 H11 H H11 N N N 0 0.34 -1.78 1.788
46 H12 H H12 N N N 0 2.61 -2.518 2.386
47 H13 H H13 N N N 0 3.59 -4.496 1.298
48 H15 H H15 N N N 0 0.03 -5.017 -0.99
49 H16 H H16 N N N 0 -4.425 -2.463 0.51
50 H17 H H17 N N N 0 -4.74 -1.721 -1.077
51 H18 H H18 N N N 0 -3.562 -3.047 -0.933
52 H19 H H19 N N N 0 -4.569 2.743 1.91
53 H20 H H20 N N N 0 -5.939 1.767 2.491
54 H21 H H21 N N N 0 -4.327 1.03 2.327
55 H22 H H22 N N N 0 -5.103 -1.122 -2.824
56 H23 H H23 N N N 0 -5.504 0.381 -3.69
57 H24 H H24 N N N 0 -3.859 0.13 -3.059
58 H25 H H25 N N N 0 -1.14 3.312 0.364
59 H26 H H26 N N N 0 0.659 4.939 0.776
60 H27 H H27 N N N 0 2.962 4.162 1.155
61 H28 H H28 N N N 0 8.549 1.166 -0.449
62 H30 H H30 N N N 0 4.557 2.431 -0.591
63 H32 H H32 N N N 0 -1.921 -3.589 -0.229



XJ4 : Chemical Bonds

Total Number of Bonds: 66
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C18 C17 C C doub 1.38 N Y
2 C18 C19 C C sing 1.38 N Y
3 C17 C16 C C sing 1.38 N Y
4 C4 N5 C N sing 1.47 N N
5 C4 C3 C C sing 1.53 N N
6 N5 C6 N C sing 1.47 N N
7 C19 C14 C C doub 1.39 N Y
8 C16 C15 C C doub 1.38 N Y
9 N2 C3 N C sing 1.47 N N
10 N2 C1 N C sing 1.47 N N
11 C33 C32 C C doub 1.38 N Y
12 C33 C7 C C sing 1.38 N Y
13 C32 C31 C C sing 1.38 N Y
14 C14 C15 C C sing 1.39 N Y
15 C14 N13 C N sing 1.4 N N
16 C6 C7 C C sing 1.51 N N
17 C7 C8 C C doub 1.38 N Y
18 C31 C9 C C doub 1.39 N Y
19 C8 C9 C C sing 1.39 N Y
20 C9 C10 C C sing 1.48 N N
21 N13 C12 N C sing 1.39 N N
22 N11 C10 N C doub 1.33 N Y
23 N11 C12 N C sing 1.33 N Y
24 C10 N30 C N sing 1.32 N Y
25 C12 C20 C C doub 1.39 N Y
26 N30 C22 N C doub 1.33 N Y
27 C20 C22 C C sing 1.4 N Y
28 C20 C21 C C sing 1.51 N N
29 C29 C28 C C sing 1.51 N N
30 C22 C23 C C sing 1.48 N N
31 C28 C23 C C sing 1.42 N Y
32 C28 N27 C N doub 1.3 N Y
33 C23 C24 C C doub 1.37 N Y
34 N27 O26 N O sing 1.21 N Y
35 C24 C25 C C sing 1.51 N N
36 C24 O26 C O sing 1.34 N Y
37 C1 H1 C H sing 1.09 N N
38 C1 H2 C H sing 1.09 N N
39 C1 H3 C H sing 1.09 N N
40 C3 H4 C H sing 1.09 N N
41 C3 H5 C H sing 1.09 N N
42 C4 H6 C H sing 1.09 N N
43 C4 H7 C H sing 1.09 N N
44 C6 H8 C H sing 1.09 N N
45 C6 H9 C H sing 1.09 N N
46 C8 H10 C H sing 1.08 N N
47 C15 H11 C H sing 1.08 N N
48 C16 H12 C H sing 1.08 N N
49 C17 H13 C H sing 1.08 N N
50 C18 H14 C H sing 1.08 N N
51 C19 H15 C H sing 1.08 N N
52 C21 H16 C H sing 1.09 N N
53 C21 H17 C H sing 1.09 N N
54 C21 H18 C H sing 1.09 N N
55 C25 H19 C H sing 1.09 N N
56 C25 H20 C H sing 1.09 N N
57 C25 H21 C H sing 1.09 N N
58 C29 H22 C H sing 1.09 N N
59 C29 H23 C H sing 1.09 N N
60 C29 H24 C H sing 1.09 N N
61 C31 H25 C H sing 1.08 N N
62 C32 H26 C H sing 1.08 N N
63 C33 H27 C H sing 1.08 N N
64 N2 H28 N H sing 1.01 N N
65 N5 H30 N H sing 1.01 N N
66 N13 H32 N H sing 0.97 N N



XJ4 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
XJ4 7faj Open in New Window Bound ligand 4 1