Chemical Components in the PDB

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7KD : Summary

Code

7KD

One-letter code

X

Molecule name

~{N}-methyl-4-[[4-[[3-[methyl(methylsulfonyl)amino]pyrazin-2-yl]methylamino]-5-(trifluoromethyl)pyrimidin-2-yl]amino]benzamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 ~{N}-methyl-4-[[4-[[3-[methyl(methylsulfonyl)amino]pyrazin-2-yl]methylamino]-5-(trifluoromethyl)pyrimidin-2-yl]amino]benzamide

Formula

C20 H21 F3 N8 O3 S

Formal charge

0

Molecular weight

510.493 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CNC(=O)c1ccc(Nc2ncc(c(NCc3nccnc3N(C)[S](C)(=O)=O)n2)C(F)(F)F)cc1
SMILES OpenEye OEToolkits 2.0.6 CNC(=O)c1ccc(cc1)Nc2ncc(c(n2)NCc3c(nccn3)N(C)S(=O)(=O)C)C(F)(F)F
Canonical SMILES CACTVS 3.385 CNC(=O)c1ccc(Nc2ncc(c(NCc3nccnc3N(C)[S](C)(=O)=O)n2)C(F)(F)F)cc1
Canonical SMILES OpenEye OEToolkits 2.0.6 CNC(=O)c1ccc(cc1)Nc2ncc(c(n2)NCc3c(nccn3)N(C)S(=O)(=O)C)C(F)(F)F

IUPAC InChI

InChI=1S/C20H21F3N8O3S/c1-24-18(32)12-4-6-13(7-5-12)29-19-28-10-14(20(21,22)23)16(30-19)27-11-15-17(26-9-8-25-15)31(2)35(3,33)34/h4-10H,11H2,1-3H3,(H,24,32)(H2,27,28,29,30)

IUPAC InChI key

FWLMVFUGMHIOAA-UHFFFAOYSA-N
7KD

wwPDB Information

Atom count

56 (35 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2016-11-04

Last modified at

2017-12-01

Status

Released

Obsoleted

Not Assigned



7KD : Atoms of Molecule

Total Number of Atoms: 56
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 -0.041 2.129 0.427
2 C2 C C2 N Y N 0 -0.57 1.025 -0.246
3 C8 C C3 N N N 0 -0.934 3.258 0.874
4 C13 C C4 N Y N 0 3.75 -0.817 -0.607
5 C14 C C5 N Y N 0 4.372 0.419 -0.754
6 C15 C C6 N Y N 0 5.735 0.529 -0.595
7 C16 C C7 N Y N 0 6.494 -0.604 -0.285
8 C19 C C8 N N N 0 7.955 -0.49 -0.112
9 C22 C C9 N N N 0 10.135 -1.469 0.358
10 C24 C C10 N Y N 0 -3.957 -0.047 -1.396
11 N26 N N1 N Y N 0 -6.131 -0.277 -0.526
12 C27 C C11 N Y N 0 -6.61 0.227 -1.651
13 N29 N N2 N Y N 0 -4.442 0.465 -2.511
14 C32 C C12 N N N 0 -4.061 -0.083 1.954
15 C33 C C13 N N N 0 -5.546 -3.304 1.526
16 N20 N N3 N N N 0 8.685 -1.582 0.187
17 O21 O O1 N N N 0 8.5 0.59 -0.241
18 C17 C C14 N Y N 0 5.865 -1.844 -0.137
19 C18 C C15 N Y N 0 4.502 -1.946 -0.298
20 N12 N N4 N N N 0 2.37 -0.923 -0.764
21 C4 C C16 N Y N 0 1.545 0.114 -0.36
22 N3 N N5 N Y N 0 0.248 0.046 -0.62
23 N5 N N6 N Y N 0 2.073 1.149 0.276
24 C6 C C17 N Y N 0 1.317 2.16 0.678
25 F10 F F1 N N N 0 -0.165 4.233 1.519
26 F11 F F2 N N N 0 -1.564 3.823 -0.239
27 F9 F F3 N N N 0 -1.9 2.766 1.758
28 N7 N N7 N N N 0 -1.926 0.951 -0.519
29 C23 C C18 N N N 0 -2.468 -0.212 -1.226
30 C28 C C19 N Y N 0 -5.747 0.61 -2.661
31 C25 C C20 N Y N 0 -4.822 -0.429 -0.373
32 N30 N N8 N N N 0 -4.315 -0.959 0.808
33 S31 S S1 N N N 0 -3.998 -2.58 0.919
34 O34 O O2 N N N 0 -2.983 -2.672 1.909
35 O35 O O3 N N N 0 -3.751 -2.982 -0.422
36 H1 H H1 N N N 0 3.785 1.293 -0.994
37 H2 H H2 N N N 0 6.217 1.488 -0.71
38 H3 H H3 N N N 0 10.582 -1.099 -0.565
39 H4 H H4 N N N 0 10.353 -0.776 1.171
40 H5 H H5 N N N 0 10.551 -2.449 0.595
41 H6 H H6 N N N 0 -7.675 0.351 -1.776
42 H7 H H7 N N N 0 -4.922 -0.1 2.622
43 H8 H H8 N N N 0 -3.178 -0.432 2.489
44 H9 H H9 N N N 0 -3.894 0.936 1.603
45 H10 H H10 N N N 0 -5.795 -2.871 2.494
46 H11 H H11 N N N 0 -6.348 -3.094 0.817
47 H12 H H12 N N N 0 -5.427 -4.383 1.63
48 H13 H H13 N N N 0 8.25 -2.443 0.289
49 H14 H H14 N N N 0 6.449 -2.72 0.103
50 H15 H H15 N N N 0 4.016 -2.904 -0.184
51 H16 H H16 N N N 0 1.987 -1.724 -1.156
52 H17 H H17 N N N 0 1.757 2.999 1.196
53 H18 H H18 N N N 0 -2.516 1.669 -0.243
54 H19 H H19 N N N 0 -2.266 -1.114 -0.649
55 H20 H H20 N N N 0 -1.997 -0.294 -2.205
56 H21 H H21 N N N 0 -6.141 1.029 -3.575



7KD : Chemical Bonds

Total Number of Bonds: 58
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C33 S31 C S sing 1.81 N N
2 O35 S31 O S doub 1.42 N N
3 S31 O34 S O doub 1.42 N N
4 S31 N30 S N sing 1.66 N N
5 C32 N30 C N sing 1.46 N N
6 N26 C27 N C doub 1.32 N Y
7 N26 C25 N C sing 1.33 N Y
8 N30 C25 N C sing 1.39 N N
9 F9 C8 F C sing 1.4 N N
10 C27 C28 C C sing 1.38 N Y
11 C25 C24 C C doub 1.39 N Y
12 F11 C8 F C sing 1.4 N N
13 F10 C8 F C sing 1.4 N N
14 C8 C1 C C sing 1.51 N N
15 C28 N29 C N doub 1.32 N Y
16 C24 N29 C N sing 1.32 N Y
17 C24 C23 C C sing 1.51 N N
18 N7 C23 N C sing 1.46 N N
19 N7 C2 N C sing 1.39 N N
20 C1 C2 C C doub 1.4 N Y
21 C1 C6 C C sing 1.38 N Y
22 C2 N3 C N sing 1.33 N Y
23 C6 N5 C N doub 1.32 N Y
24 N3 C4 N C doub 1.32 N Y
25 N5 C4 N C sing 1.32 N Y
26 C4 N12 C N sing 1.39 N N
27 C18 C17 C C doub 1.38 N Y
28 C18 C13 C C sing 1.39 N Y
29 N12 C13 N C sing 1.39 N N
30 C17 C16 C C sing 1.4 N Y
31 C13 C14 C C doub 1.39 N Y
32 C16 C19 C C sing 1.48 N N
33 C16 C15 C C doub 1.4 N Y
34 C14 C15 C C sing 1.38 N Y
35 O21 C19 O C doub 1.22 N N
36 C19 N20 C N sing 1.35 N N
37 N20 C22 N C sing 1.46 N N
38 C14 H1 C H sing 1.08 N N
39 C15 H2 C H sing 1.08 N N
40 C22 H3 C H sing 1.09 N N
41 C22 H4 C H sing 1.09 N N
42 C22 H5 C H sing 1.09 N N
43 C27 H6 C H sing 1.08 N N
44 C32 H7 C H sing 1.09 N N
45 C32 H8 C H sing 1.09 N N
46 C32 H9 C H sing 1.09 N N
47 C33 H10 C H sing 1.09 N N
48 C33 H11 C H sing 1.09 N N
49 C33 H12 C H sing 1.09 N N
50 N20 H13 N H sing 0.97 N N
51 C17 H14 C H sing 1.08 N N
52 C18 H15 C H sing 1.08 N N
53 N12 H16 N H sing 0.97 N N
54 C6 H17 C H sing 1.08 N N
55 N7 H18 N H sing 0.97 N N
56 C23 H19 C H sing 1.09 N N
57 C23 H20 C H sing 1.09 N N
58 C28 H21 C H sing 1.08 N N



7KD : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
7KD 5mah Open in New Window Bound ligand 1 1