Chemical Components in the PDB

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R6K : Summary

Code

R6K

One-letter code

X

Molecule name

2-azanyl-~{N}-[(1~{S},2~{S})-2-[[4-[4-[(4-methylpiperazin-1-yl)methyl]phenyl]phenyl]methoxy]cyclopentyl]-5-(1-methylpyrazol-4-yl)pyridine-3-carboxamide

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 2-azanyl-~{N}-[(1~{S},2~{S})-2-[[4-[4-[(4-methylpiperazin-1-yl)methyl]phenyl]phenyl]methoxy]cyclopentyl]-5-(1-methylpyrazol-4-yl)pyridine-3-carboxamide

Formula

C34 H41 N7 O2

Formal charge

0

Molecular weight

579.735 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CN1CCN(CC1)Cc2ccc(cc2)c3ccc(CO[CH]4CCC[CH]4NC(=O)c5cc(cnc5N)c6cnn(C)c6)cc3
SMILES OpenEye OEToolkits 2.0.7 Cn1cc(cn1)c2cc(c(nc2)N)C(=O)NC3CCCC3OCc4ccc(cc4)c5ccc(cc5)CN6CCN(CC6)C
Canonical SMILES CACTVS 3.385 CN1CCN(CC1)Cc2ccc(cc2)c3ccc(CO[C@H]4CCC[C@@H]4NC(=O)c5cc(cnc5N)c6cnn(C)c6)cc3
Canonical SMILES OpenEye OEToolkits 2.0.7 Cn1cc(cn1)c2cc(c(nc2)N)C(=O)N[C@H]3CCC[C@@H]3OCc4ccc(cc4)c5ccc(cc5)CN6CCN(CC6)C

IUPAC InChI

InChI=1S/C34H41N7O2/c1-39-14-16-41(17-15-39)21-24-6-10-26(11-7-24)27-12-8-25(9-13-27)23-43-32-5-3-4-31(32)38-34(42)30-18-28(19-36-33(30)35)29-20-37-40(2)22-29/h6-13,18-20,22,31-32H,3-5,14-17,21,23H2,1-2H3,(H2,35,36)(H,38,42)/t31-,32-/m0/s1

IUPAC InChI key

GTVWQFJFCAUNFY-ACHIHNKUSA-N
R6K

wwPDB Information

Atom count

84 (43 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-09-07

Last modified at

2020-10-30

Status

Released

Obsoleted

Not Assigned



R6K : Atoms of Molecule

Total Number of Atoms: 84
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 10.424 1.911 2.04
2 C2 C C2 N N N 0 10.009 2.183 0.592
3 C3 C C3 N N N 0 8.287 1.763 -1.058
4 N6 N N1 N Y N 0 -8.231 3.856 -1.414
5 C7 C C4 N Y N 0 4.334 0.216 -1.564
6 C8 C C5 N Y N 0 4.522 1.514 -1.095
7 C9 C C6 N Y N 0 5.8 2.008 -0.933
8 C10 C C7 N Y N 0 2.962 -0.319 -1.746
9 C11 C C8 N Y N 0 2.774 -1.618 -2.215
10 C12 C C9 N Y N 0 1.495 -2.112 -2.377
11 C13 C C10 N Y N 0 0.402 -1.321 -2.074
12 C14 C C11 N N N 0 -0.992 -1.867 -2.251
13 C15 C C12 S N N 0 -2.73 -3.053 -1.104
14 C16 C C13 N N N 0 -2.662 -4.523 -1.555
15 C19 C C14 S N N 0 -3.37 -3.052 0.3
16 C20 C C15 N N N 0 -4.581 -1.458 1.689
17 C21 C C16 N Y N 0 -5.476 -0.297 1.847
18 C22 C C17 N Y N 0 -5.899 0.431 0.732
19 C24 C C18 N Y N 0 -7.138 1.844 2.233
20 C27 C C19 N Y N 0 -6.898 2.116 -1.571
21 C30 C C20 N Y N 0 0.582 -0.031 -1.607
22 C31 C C21 N Y N 0 1.857 0.473 -1.442
23 C32 C C22 N N N 0 8.926 0.02 0.498
24 C33 C C23 N N N 0 9.34 -0.251 1.946
25 O1 O O1 N N N 0 -4.133 -2.019 2.671
26 C25 C C24 N Y N 0 -5.923 0.092 3.122
27 N4 N N2 N N N 0 -5.519 -0.62 4.237
28 N3 N N3 N Y N 0 -6.727 1.135 3.265
29 C26 C C26 N Y N 0 -7.217 2.33 -0.216
30 C23 C C25 N Y N 0 -6.745 1.52 0.936
31 C29 C C27 N Y N 0 -8.038 3.418 -0.153
32 C28 C C28 N N N 0 -9.05 5.005 -1.808
33 N5 N N4 N Y N 0 -7.509 3.027 -2.281
34 N2 N N5 N N N 0 -4.259 -1.899 0.457
35 C18 C C29 N N N 0 -4.18 -4.372 0.348
36 C17 C C30 N N N 0 -3.263 -5.363 -0.41
37 O O O2 N N N 0 -1.414 -2.499 -1.041
38 C6 C C31 N Y N 0 5.439 -0.577 -1.868
39 C5 C C32 N Y N 0 6.713 -0.072 -1.703
40 C4 C C33 N Y N 0 6.894 1.217 -1.236
41 N1 N N6 N N N 0 8.759 1.467 0.301
42 N N N7 N N N 0 10.591 0.465 2.237
43 C C C34 N N N 0 11.062 0.169 3.596
44 H1 H H1 N N N 0 11.366 2.418 2.25
45 H2 H H2 N N N 0 9.653 2.284 2.715
46 H3 H H3 N N N 0 9.857 3.253 0.452
47 H4 H H4 N N N 0 10.793 1.835 -0.082
48 H5 H H5 N N N 0 8.955 1.298 -1.784
49 H6 H H6 N N N 0 8.278 2.842 -1.213
50 H7 H H7 N N N 0 3.669 2.132 -0.858
51 H8 H H8 N N N 0 5.947 3.014 -0.569
52 H9 H H9 N N N 0 3.627 -2.236 -2.452
53 H10 H H10 N N N 0 1.349 -3.118 -2.741
54 H11 H H11 N N N 0 -1.673 -1.051 -2.492
55 H12 H H12 N N N 0 -0.996 -2.595 -3.063
56 H13 H H13 N N N 0 -3.344 -2.478 -1.796
57 H14 H H14 N N N 0 -3.244 -4.661 -2.466
58 H15 H H15 N N N 0 -1.625 -4.813 -1.727
59 H16 H H16 N N N 0 -2.6 -3.049 1.071
60 H17 H H17 N N N 0 -5.578 0.157 -0.263
61 H18 H H18 N N N 0 -7.793 2.687 2.395
62 H19 H H19 N N N 0 -6.265 1.33 -1.956
63 H20 H H20 N N N 0 -0.275 0.582 -1.373
64 H21 H H21 N N N 0 1.997 1.479 -1.074
65 H25 H H25 N N N 0 9.493 -1.321 2.086
66 H22 H H22 N N N 0 9.697 -0.352 -0.177
67 H23 H H23 N N N 0 7.984 -0.486 0.288
68 H24 H H24 N N N 0 8.557 0.097 2.619
69 H26 H H26 N N N 0 -4.868 -1.334 4.147
70 H27 H H27 N N N 0 -5.887 -0.406 5.109
71 H28 H H28 N N N 0 -8.458 3.849 0.743
72 H29 H H29 N N N 0 -8.434 5.904 -1.818
73 H30 H H30 N N N 0 -9.46 4.835 -2.804
74 H31 H H31 N N N 0 -9.866 5.132 -1.096
75 H32 H H32 N N N 0 -4.617 -1.452 -0.326
76 H33 H H33 N N N 0 -4.33 -4.695 1.378
77 H34 H H34 N N N 0 -5.135 -4.258 -0.165
78 H35 H H35 N N N 0 -3.847 -6.192 -0.812
79 H36 H H36 N N N 0 -2.476 -5.733 0.246
80 H37 H H37 N N N 0 5.299 -1.584 -2.232
81 H38 H H38 N N N 0 7.57 -0.685 -1.938
82 H41 H H41 N N N 0 10.337 0.539 4.321
83 H42 H H42 N N N 0 11.177 -0.909 3.714
84 H43 H H43 N N N 0 12.023 0.657 3.761



R6K : Chemical Bonds

Total Number of Bonds: 89
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C28 N6 C N sing 1.46 N N
2 N5 N6 N N sing 1.4 N Y
3 N5 C27 N C doub 1.31 N Y
4 N6 C29 N C sing 1.35 N Y
5 C27 C26 C C sing 1.41 N Y
6 C29 C26 C C doub 1.36 N Y
7 C26 C23 C C sing 1.49 N N
8 C24 C23 C C doub 1.39 N Y
9 C24 N3 C N sing 1.32 N Y
10 C23 C22 C C sing 1.39 N Y
11 N3 C25 N C doub 1.32 N Y
12 C22 C21 C C doub 1.4 N Y
13 C25 C21 C C sing 1.41 N Y
14 C25 N4 C N sing 1.38 N N
15 C21 C20 C C sing 1.47 N N
16 C20 O1 C O doub 1.22 N N
17 C20 N2 C N sing 1.35 N N
18 N2 C19 N C sing 1.46 N N
19 C19 C18 C C sing 1.55 N N
20 C19 C15 C C sing 1.54 N N
21 C18 C17 C C sing 1.55 N N
22 C15 C16 C C sing 1.54 N N
23 C15 O C O sing 1.43 N N
24 C17 C16 C C sing 1.54 N N
25 C14 O C O sing 1.43 N N
26 C14 C13 C C sing 1.51 N N
27 C12 C13 C C doub 1.38 N Y
28 C12 C11 C C sing 1.38 N Y
29 C13 C30 C C sing 1.38 N Y
30 C11 C10 C C doub 1.39 N Y
31 C30 C31 C C doub 1.38 N Y
32 C10 C31 C C sing 1.39 N Y
33 C10 C7 C C sing 1.48 N N
34 C7 C6 C C doub 1.39 N Y
35 C7 C8 C C sing 1.39 N Y
36 C6 C5 C C sing 1.38 N Y
37 C8 C9 C C doub 1.38 N Y
38 C5 C4 C C doub 1.38 N Y
39 C9 C4 C C sing 1.38 N Y
40 C4 C3 C C sing 1.51 N N
41 C3 N1 C N sing 1.47 N N
42 N1 C2 N C sing 1.47 N N
43 N1 C32 N C sing 1.47 N N
44 C2 C1 C C sing 1.53 N N
45 C32 C33 C C sing 1.53 N N
46 C1 N C N sing 1.47 N N
47 C33 N C N sing 1.47 N N
48 N C N C sing 1.47 N N
49 C1 H1 C H sing 1.09 N N
50 C1 H2 C H sing 1.09 N N
51 C2 H3 C H sing 1.09 N N
52 C2 H4 C H sing 1.09 N N
53 C3 H5 C H sing 1.09 N N
54 C3 H6 C H sing 1.09 N N
55 C8 H7 C H sing 1.08 N N
56 C9 H8 C H sing 1.08 N N
57 C11 H9 C H sing 1.08 N N
58 C12 H10 C H sing 1.08 N N
59 C14 H11 C H sing 1.09 N N
60 C14 H12 C H sing 1.09 N N
61 C15 H13 C H sing 1.09 N N
62 C16 H14 C H sing 1.09 N N
63 C16 H15 C H sing 1.09 N N
64 C19 H16 C H sing 1.09 N N
65 C22 H17 C H sing 1.08 N N
66 C24 H18 C H sing 1.08 N N
67 C27 H19 C H sing 1.08 N N
68 C30 H20 C H sing 1.08 N N
69 C31 H21 C H sing 1.08 N N
70 C32 H22 C H sing 1.09 N N
71 C32 H23 C H sing 1.09 N N
72 C33 H24 C H sing 1.09 N N
73 C33 H25 C H sing 1.09 N N
74 N4 H26 N H sing 0.97 N N
75 N4 H27 N H sing 0.97 N N
76 C29 H28 C H sing 1.08 N N
77 C28 H29 C H sing 1.09 N N
78 C28 H30 C H sing 1.09 N N
79 C28 H31 C H sing 1.09 N N
80 N2 H32 N H sing 0.97 N N
81 C18 H33 C H sing 1.09 N N
82 C18 H34 C H sing 1.09 N N
83 C17 H35 C H sing 1.09 N N
84 C17 H36 C H sing 1.09 N N
85 C6 H37 C H sing 1.08 N N
86 C5 H38 C H sing 1.08 N N
87 C H41 C H sing 1.09 N N
88 C H42 C H sing 1.09 N N
89 C H43 C H sing 1.09 N N



R6K : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
R6K 7aaz Open in New Window Bound ligand 1 1