Chemical Components in the PDB

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8RC : Summary

Code

8RC

One-letter code

X

Molecule name

6-ethyl-3-[[4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]amino]-5-[(3R)-1-prop-2-enoylpyrrolidin-3-yl]oxy-pyrazin e-2-carboxamide

Synonyms

Naquotinib

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.6 6-ethyl-3-[[4-[4-(4-methylpiperazin-1-yl)piperidin-1-yl]phenyl]amino]-5-[(3~{R})-1-prop-2-enoylpyrrolidin-3-yl]oxy-pyrazine-2-carboxamide

Formula

C30 H42 N8 O3

Formal charge

0

Molecular weight

562.706 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CCc1nc(C(N)=O)c(Nc2ccc(cc2)N3CCC(CC3)N4CCN(C)CC4)nc1O[CH]5CCN(C5)C(=O)C=C
SMILES OpenEye OEToolkits 2.0.6 CCc1c(nc(c(n1)C(=O)N)Nc2ccc(cc2)N3CCC(CC3)N4CCN(CC4)C)OC5CCN(C5)C(=O)C=C
Canonical SMILES CACTVS 3.385 CCc1nc(C(N)=O)c(Nc2ccc(cc2)N3CCC(CC3)N4CCN(C)CC4)nc1O[C@@H]5CCN(C5)C(=O)C=C
Canonical SMILES OpenEye OEToolkits 2.0.6 CCc1c(nc(c(n1)C(=O)N)Nc2ccc(cc2)N3CCC(CC3)N4CCN(CC4)C)O[C@@H]5CCN(C5)C(=O)C=C

IUPAC InChI

InChI=1S/C30H42N8O3/c1-4-25-30(41-24-12-15-38(20-24)26(39)5-2)34-29(27(33-25)28(31)40)32-21-6-8-22(9-7-21)36-13-10-23(11-14-36)37-18-16-35(3)17-19-37/h5-9,23-24H,2,4,10-20H2,1,3H3,(H2,31,40)(H,32,34)/t24-/m1/s1

IUPAC InChI key

QKDCLUARMDUUKN-XMMPIXPASA-N
8RC

wwPDB Information

Atom count

83 (41 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2017-08-31

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



8RC : Atoms of Molecule

Total Number of Atoms: 83
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C12 C C1 N Y N 0 0.418 2.85 -0.446
2 C14 C C2 N Y N 0 0.003 0.598 0.29
3 C11 C C3 N Y N 0 -0.924 3.144 -0.303
4 C15 C C4 N Y N 0 -1.339 0.89 0.428
5 C13 C C5 N Y N 0 0.885 1.575 -0.153
6 C10 C C6 N Y N 0 -1.806 2.165 0.134
7 C1 C C7 N Y N 0 -5.481 1.783 0.154
8 C5 C C8 N Y N 0 -6.002 -0.429 -0.159
9 C2 C C9 N Y N 0 -4.113 1.465 0.131
10 C4 C C10 N Y N 0 -4.642 -0.748 -0.177
11 C29 C C11 N N N 0 -5.913 3.181 0.337
12 C38 C C12 N N N 0 0.203 -3.508 1.017
13 C18 C C13 N N N 0 3.978 -0.453 -0.255
14 C20 C C14 N N N 0 4.553 1.937 0.174
15 C37 C C15 N N N 0 -2.647 -3.567 -1.4
16 C17 C C16 N N N 0 2.518 -0.12 0.06
17 C21 C C17 N N N 0 3.076 2.201 0.475
18 C36 C C18 N N N 0 -1.229 -4.008 -0.98
19 C23 C C19 N N N 0 6.571 0.556 -1.21
20 C27 C C20 N N N 0 7.207 0.926 1.096
21 C24 C C21 N N N 0 8.016 0.181 -1.548
22 C26 C C22 N N N 0 8.651 0.551 0.758
23 C34 C C23 N N N 0 -2.123 -2.602 0.737
24 C19 C C24 N N N 0 4.892 0.488 0.534
25 C33 C C25 R N N 0 -2.862 -2.266 -0.582
26 C32 C C26 N N N 0 -7.351 -1.689 -1.814
27 C41 C C27 N N N 0 2.436 -4.446 1.169
28 C28 C C28 N N N 0 10.33 0.618 -0.986
29 C9 C C29 N N N 0 -7.03 -1.517 -0.328
30 C40 C C30 N N N 0 1.304 -4.324 0.482
31 N6 N N1 N Y N 0 -6.387 0.818 0.004
32 N3 N N2 N Y N 0 -3.732 0.204 -0.034
33 N16 N N3 N N N 0 2.243 1.276 -0.304
34 N35 N N4 N N N 0 -0.945 -3.384 0.32
35 N22 N N5 N N N 0 6.294 0.213 0.192
36 N25 N N6 N N N 0 8.929 0.894 -0.644
37 N31 N N7 N N N 0 -7.219 3.465 0.517
38 N7 N N8 N N N 0 -3.167 2.463 0.28
39 O30 O O1 N N N 0 -5.092 4.077 0.325
40 O39 O O2 N N N 0 0.327 -2.945 2.088
41 O8 O O3 N N N 0 -4.252 -2.035 -0.345
42 H1 H H1 N N N 0 1.103 3.61 -0.791
43 H2 H H2 N N N 0 0.366 -0.393 0.519
44 H3 H H3 N N N 0 -1.287 4.135 -0.531
45 H4 H H4 N N N 0 -2.025 0.13 0.772
46 H5 H H5 N N N 0 4.186 -1.485 0.03
47 H6 H H6 N N N 0 4.159 -0.326 -1.322
48 H7 H H7 N N N 0 4.742 2.102 -0.887
49 H8 H H8 N N N 0 5.172 2.614 0.763
50 H9 H H9 N N N 0 -2.685 -3.36 -2.47
51 H10 H H10 N N N 0 -3.383 -4.322 -1.125
52 H11 H H11 N N N 0 1.864 -0.78 -0.511
53 H12 H H12 N N N 0 2.334 -0.261 1.125
54 H13 H H13 N N N 0 2.89 2.049 1.539
55 H14 H H14 N N N 0 2.828 3.227 0.206
56 H15 H H15 N N N 0 -1.19 -5.093 -0.888
57 H16 H H16 N N N 0 -0.502 -3.671 -1.72
58 H17 H H17 N N N 0 6.429 1.626 -1.357
59 H18 H H18 N N N 0 5.891 0.006 -1.86
60 H19 H H19 N N N 0 6.99 0.646 2.127
61 H20 H H20 N N N 0 7.072 2.001 0.976
62 H21 H H21 N N N 0 8.15 -0.894 -1.427
63 H22 H H22 N N N 0 8.232 0.46 -2.579
64 H23 H H23 N N N 0 9.332 1.101 1.409
65 H24 H H24 N N N 0 8.793 -0.52 0.905
66 H25 H H25 N N N 0 -1.812 -1.687 1.241
67 H26 H H26 N N N 0 -2.761 -3.197 1.391
68 H27 H H27 N N N 0 4.74 0.334 1.602
69 H28 H H28 N N N 0 -2.405 -1.411 -1.079
70 H29 H H29 N N N 0 -7.743 -0.753 -2.212
71 H30 H H30 N N N 0 -6.443 -1.961 -2.352
72 H31 H H31 N N N 0 -8.095 -2.476 -1.936
73 H32 H H32 N N N 0 3.244 -5.044 0.777
74 H33 H H33 N N N 0 2.547 -3.946 2.12
75 H35 H H35 N N N 0 10.539 -0.442 -0.837
76 H36 H H36 N N N 0 10.508 0.881 -2.029
77 H40 H H40 N N N 0 1.193 -4.823 -0.469
78 H37 H H37 N N N 0 10.984 1.21 -0.345
79 H38 H H38 N N N 0 -6.639 -2.453 0.07
80 H39 H H39 N N N 0 -7.938 -1.245 0.21
81 H44 H H44 N N N 0 -7.874 2.749 0.527
82 H45 H H45 N N N 0 -7.503 4.384 0.638
83 H46 H H46 N N N 0 -3.445 3.369 0.485



8RC : Chemical Bonds

Total Number of Bonds: 87
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C32 C9 C C sing 1.53 N N
2 C9 C5 C C sing 1.51 N N
3 C5 N6 C N doub 1.32 N Y
4 C5 C4 C C sing 1.4 N Y
5 N6 C1 N C sing 1.33 N Y
6 N31 C29 N C sing 1.35 N N
7 O8 C4 O C sing 1.36 N N
8 O8 C33 O C sing 1.43 N N
9 C4 N3 C N doub 1.32 N Y
10 C1 C29 C C sing 1.47 N N
11 C1 C2 C C doub 1.4 N Y
12 C29 O30 C O doub 1.22 N N
13 C37 C33 C C sing 1.55 N N
14 C37 C36 C C sing 1.54 N N
15 O39 C38 O C doub 1.22 N N
16 C33 C34 C C sing 1.55 N N
17 C36 N35 C N sing 1.47 N N
18 N3 C2 N C sing 1.33 N Y
19 C34 N35 C N sing 1.47 N N
20 C2 N7 C N sing 1.38 N N
21 N35 C38 N C sing 1.35 N N
22 C38 C40 C C sing 1.47 N N
23 N7 C10 N C sing 1.4 N N
24 C40 C41 C C doub 1.33 N N
25 C10 C11 C C doub 1.39 N Y
26 C10 C15 C C sing 1.39 N Y
27 C11 C12 C C sing 1.38 N Y
28 C15 C14 C C doub 1.38 N Y
29 C12 C13 C C doub 1.39 N Y
30 C14 C13 C C sing 1.39 N Y
31 C13 N16 C N sing 1.4 N N
32 N16 C17 N C sing 1.47 N N
33 N16 C21 N C sing 1.47 N N
34 C17 C18 C C sing 1.53 N N
35 C21 C20 C C sing 1.53 N N
36 C18 C19 C C sing 1.53 N N
37 C20 C19 C C sing 1.53 N N
38 C19 N22 C N sing 1.47 N N
39 N22 C27 N C sing 1.47 N N
40 N22 C23 N C sing 1.47 N N
41 C27 C26 C C sing 1.53 N N
42 C23 C24 C C sing 1.53 N N
43 C26 N25 C N sing 1.47 N N
44 N25 C24 N C sing 1.47 N N
45 N25 C28 N C sing 1.47 N N
46 C12 H1 C H sing 1.08 N N
47 C14 H2 C H sing 1.08 N N
48 C11 H3 C H sing 1.08 N N
49 C15 H4 C H sing 1.08 N N
50 C18 H5 C H sing 1.09 N N
51 C18 H6 C H sing 1.09 N N
52 C20 H7 C H sing 1.09 N N
53 C20 H8 C H sing 1.09 N N
54 C37 H9 C H sing 1.09 N N
55 C37 H10 C H sing 1.09 N N
56 C17 H11 C H sing 1.09 N N
57 C17 H12 C H sing 1.09 N N
58 C21 H13 C H sing 1.09 N N
59 C21 H14 C H sing 1.09 N N
60 C36 H15 C H sing 1.09 N N
61 C36 H16 C H sing 1.09 N N
62 C23 H17 C H sing 1.09 N N
63 C23 H18 C H sing 1.09 N N
64 C27 H19 C H sing 1.09 N N
65 C27 H20 C H sing 1.09 N N
66 C24 H21 C H sing 1.09 N N
67 C24 H22 C H sing 1.09 N N
68 C26 H23 C H sing 1.09 N N
69 C26 H24 C H sing 1.09 N N
70 C34 H25 C H sing 1.09 N N
71 C34 H26 C H sing 1.09 N N
72 C19 H27 C H sing 1.09 N N
73 C33 H28 C H sing 1.09 N N
74 C32 H29 C H sing 1.09 N N
75 C32 H30 C H sing 1.09 N N
76 C32 H31 C H sing 1.09 N N
77 C41 H32 C H sing 1.08 N N
78 C41 H33 C H sing 1.08 N N
79 C28 H35 C H sing 1.09 N N
80 C28 H36 C H sing 1.09 N N
81 C28 H37 C H sing 1.09 N N
82 C9 H38 C H sing 1.09 N N
83 C9 H39 C H sing 1.09 N N
84 C40 H40 C H sing 1.08 N N
85 N31 H44 N H sing 0.97 N N
86 N31 H45 N H sing 0.97 N N
87 N7 H46 N H sing 0.97 N N



8RC : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
8RC 5y9t Open in New Window Bound ligand 1 1
8RC 7lg8 Open in New Window Bound ligand 4 1