Chemical Components in the PDB

pdbe.org/chem
spacer

083 : Summary

Code

083

One-letter code

X

Molecule name

4,6-dimethyl-N'-(3-pyridin-2-ylisoquinolin-1-yl)pyrimidine-2-carboximidamide

Systematic names

ProgramVersionName
ACDLabs 12.01 4,6-dimethyl-N'-[3-(pyridin-2-yl)isoquinolin-1-yl]pyrimidine-2-carboximidamide
OpenEye OEToolkits 1.9.2 4,6-dimethyl-N'-(3-pyridin-2-ylisoquinolin-1-yl)pyrimidine-2-carboximidamide

Formula

C21 H18 N6

Formal charge

0

Molecular weight

354.408 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n1c(cc(nc1C(=N/c4nc(c2ncccc2)cc3c4cccc3)/N)C)C
SMILES CACTVS 3.385 Cc1cc(C)nc(n1)C(N)=Nc2nc(cc3ccccc23)c4ccccn4
SMILES OpenEye OEToolkits 1.9.2 Cc1cc(nc(n1)C(=Nc2c3ccccc3cc(n2)c4ccccn4)N)C
Canonical SMILES CACTVS 3.385 Cc1cc(C)nc(n1)C(N)=Nc2nc(cc3ccccc23)c4ccccn4
Canonical SMILES OpenEye OEToolkits 1.9.2 Cc1cc(nc(n1)/C(=N/c2c3ccccc3cc(n2)c4ccccn4)/N)C

IUPAC InChI

InChI=1S/C21H18N6/c1-13-11-14(2)25-21(24-13)19(22)27-20-16-8-4-3-7-15(16)12-18(26-20)17-9-5-6-10-23-17/h3-12H,1-2H3,(H2,22,26,27)

IUPAC InChI key

YKSJLEVXPOMXPZ-UHFFFAOYSA-N
083

wwPDB Information

Atom count

45 (27 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2013-03-21

Last modified at

2014-09-05

Status

Released

Obsoleted

Not Assigned



083 : Atoms of Molecule

Total Number of Atoms: 45
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 -5.382 0.352 -2.679
2 C10 C C10 N Y N 0 3.688 1.182 -0.122
3 C11 C C11 N Y N 0 3.281 2.494 -0.359
4 C12 C C12 N Y N 0 4.227 3.504 -0.348
5 C13 C C13 N Y N 0 5.552 3.168 -0.111
6 C14 C C14 N Y N 0 5.887 1.845 0.112
7 C15 C C15 N Y N 0 3.112 -1.205 0.105
8 C16 C C16 N Y N 0 2.17 -2.25 0.105
9 C17 C C17 N Y N 0 2.536 -3.585 0.333
10 C18 C C18 N Y N 0 1.577 -4.554 0.319
11 C19 C C19 N Y N 0 0.242 -4.238 0.084
12 C2 C C2 N Y N 0 -4.816 0.561 -1.298
13 C20 C C20 N Y N 0 -0.147 -2.949 -0.141
14 C21 C C21 N Y N 0 0.81 -1.93 -0.134
15 C3 C C3 N Y N 0 -5.63 0.999 -0.263
16 C4 C C4 N Y N 0 -5.067 1.178 0.993
17 C5 C C5 N N N 0 -5.913 1.653 2.147
18 C6 C C6 N Y N 0 -3.032 0.508 0.155
19 C7 C C7 N N N 0 -1.594 0.237 0.386
20 C8 C C8 N Y N 0 0.456 -0.531 -0.369
21 C9 C C9 N Y N 0 2.686 0.089 -0.125
22 H11 H H11 N N N 0 2.241 2.719 -0.544
23 H11C H H11C N N N 0 -5.297 1.277 -3.25
24 H12 H H12 N N N 0 3.941 4.531 -0.523
25 H12C H H12C N N N 0 -4.828 -0.439 -3.183
26 H13 H H13 N N N 0 6.315 3.933 -0.099
27 H13C H H13C N N N 0 -6.432 0.069 -2.602
28 H14 H H14 N N N 0 6.918 1.58 0.297
29 H15 H H15 N N N 0 4.156 -1.412 0.285
30 H17 H H17 N N N 0 3.569 -3.843 0.516
31 H18 H H18 N N N 0 1.858 -5.582 0.494
32 H19 H H19 N N N 0 -0.498 -5.025 0.079
33 H20 H H20 N N N 0 -1.186 -2.718 -0.322
34 H21N H H21N N N N 0 -1.592 0.797 2.347
35 H22N H H22N N N N 0 -0.132 0.166 1.806
36 H3 H H3 N N N 0 -6.678 1.197 -0.432
37 H51C H H51C N N N 0 -5.894 2.743 2.186
38 H52C H H52C N N N 0 -6.939 1.312 2.01
39 H53C H H53C N N N 0 -5.516 1.249 3.078
40 N1 N N1 N Y N 0 -3.782 0.927 1.165
41 N2 N N2 N N N 0 -1.053 0.419 1.635
42 N3 N N3 N N N 0 -0.836 -0.178 -0.603
43 N4 N N4 N Y N 0 1.409 0.389 -0.355
44 N5 N N5 N Y N 0 4.966 0.903 0.101
45 N6 N N6 N Y N 0 -3.536 0.333 -1.059



083 : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N2 C7 N C sing 1.3732466 N N
2 C7 C6 C C sing 1.4814337 N N
3 C7 N3 C N doub 1.3133583 N N
4 C6 N1 C N sing 1.3259566 N Y
5 C6 N6 C N doub 1.3260607 N Y
6 N1 C4 N C doub 1.320534 N Y
7 C4 C5 C C sing 1.5076661 N N
8 C4 C3 C C sing 1.3880007 N Y
9 C3 C2 C C doub 1.3876833 N Y
10 N6 C2 N C sing 1.3219323 N Y
11 C2 C1 C C sing 1.5070494 N N
12 N3 C8 N C sing 1.359643 N N
13 C8 C21 C C sing 1.4621019 N Y
14 C8 N4 C N doub 1.3246906 N Y
15 C21 C20 C C sing 1.3979481 N Y
16 C21 C16 C C doub 1.4174347 N Y
17 C20 C19 C C doub 1.3650887 N Y
18 C19 C18 C C sing 1.3918715 N Y
19 C18 C17 C C doub 1.3633921 N Y
20 C17 C16 C C sing 1.4029131 N Y
21 C16 C15 C C sing 1.4069076 N Y
22 C15 C9 C C doub 1.3815976 N Y
23 C9 N4 C N sing 1.3317766 N Y
24 C9 C10 C C sing 1.4827886 N N
25 C10 N5 C N doub 1.3269718 N Y
26 C10 C11 C C sing 1.3939735 N Y
27 N5 C14 N C sing 1.3174696 N Y
28 C14 C13 C C doub 1.3828532 N Y
29 C13 C12 C C sing 1.387332 N Y
30 C12 C11 C C doub 1.3838848 N Y
31 N2 H21N N H sing 0.96971595 N N
32 N2 H22N N H sing 0.9703046 N N
33 C5 H51C C H sing 1.090863 N N
34 C5 H52C C H sing 1.0898284 N N
35 C5 H53C C H sing 1.0897642 N N
36 C3 H3 C H sing 1.0798467 N N
37 C1 H11C C H sing 1.0903628 N N
38 C1 H12C C H sing 1.0893177 N N
39 C1 H13C C H sing 1.0901917 N N
40 C20 H20 C H sing 1.0796494 N N
41 C19 H19 C H sing 1.0802749 N N
42 C18 H18 C H sing 1.0799861 N N
43 C17 H17 C H sing 1.0803435 N N
44 C15 H15 C H sing 1.0794374 N N
45 C11 H11 C H sing 1.0800232 N N
46 C14 H14 C H sing 1.0804679 N N
47 C13 H13 C H sing 1.0805267 N N
48 C12 H12 C H sing 1.0803472 N N



083 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
083 4bfq Open in New Window Bound ligand 14 1