Chemical Components in the PDB

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PB3 : Summary

Code

PB3

One-letter code

X

Molecule name

N,N'-BIS(3-METHYLBENZYL)PYRIMIDINE-4,6-DICARBOXAMIDE

Systematic names

ProgramVersionName
ACDLabs 10.04 N,N'-bis(3-methylbenzyl)pyrimidine-4,6-dicarboxamide
OpenEye OEToolkits 1.5.0 N,N'-bis[(3-methylphenyl)methyl]pyrimidine-4,6-dicarboxamide

Formula

C22 H22 N4 O2

Formal charge

0

Molecular weight

374.436 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C(c2ncnc(C(=O)NCc1cccc(c1)C)c2)NCc3cccc(c3)C
SMILES CACTVS 3.341 Cc1cccc(CNC(=O)c2cc(ncn2)C(=O)NCc3cccc(C)c3)c1
SMILES OpenEye OEToolkits 1.5.0 Cc1cccc(c1)CNC(=O)c2cc(ncn2)C(=O)NCc3cccc(c3)C
Canonical SMILES CACTVS 3.341 Cc1cccc(CNC(=O)c2cc(ncn2)C(=O)NCc3cccc(C)c3)c1
Canonical SMILES OpenEye OEToolkits 1.5.0 Cc1cccc(c1)CNC(=O)c2cc(ncn2)C(=O)NCc3cccc(c3)C

IUPAC InChI

InChI=1S/C22H22N4O2/c1-15-5-3-7-17(9-15)12-23-21(27)19-11-20(26-14-25-19)22(28)24-13-18-8-4-6-16(2)10-18/h3-11,14H,12-13H2,1-2H3,(H,23,27)(H,24,28)

IUPAC InChI key

GTBUZLPQANSGGE-UHFFFAOYSA-N
PB3

wwPDB Information

Atom count

50 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2004-10-28

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



PB3 : Atoms of Molecule

Total Number of Atoms: 50
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 -0.558 -0.065 -1.196
2 C2 C C2 N Y N 0 -1.276 -0.001 0.0
3 C3 C C3 N Y N 0 -0.559 0.064 1.196
4 N6 N N6 N Y N 0 0.77 -0.062 -1.15
5 C7 C C7 N N N 0 1.632 -2.053 8.287
6 C8 C C8 N N N 0 1.631 2.056 -8.285
7 C9 C C9 N N N 0 -1.268 0.134 2.498
8 C11 C C11 N N N 0 -1.265 0.267 4.931
9 C12 C C12 N Y N 0 -0.257 0.329 6.05
10 C15 C C15 N N N 0 -1.267 -0.137 -2.498
11 C21 C C21 N Y N 0 0.2 0.837 -6.631
12 C24 C C24 N Y N 0 1.132 -1.607 -7.523
13 C30 C C30 N Y N 0 0.204 1.552 6.497
14 C31 C C31 N Y N 0 1.128 1.609 7.524
15 C32 C C32 N Y N 0 1.591 0.442 8.103
16 C34 C C34 N Y N 0 0.208 -0.838 6.626
17 N4 N N4 N Y N 0 0.769 0.068 1.15
18 C5 C C5 N Y N 0 1.407 0.001 0.0
19 N10 N N10 N N N 0 -0.565 0.197 3.646
20 N16 N N16 N N N 0 -0.564 -0.199 -3.646
21 C17 C C17 N N N 0 -1.264 -0.27 -4.931
22 C18 C C18 N Y N 0 -0.256 -0.33 -6.049
23 C4 C C4 N Y N 0 1.128 0.783 -7.654
24 C23 C C23 N Y N 0 1.593 -0.439 -8.102
25 C25 C C25 N Y N 0 0.207 -1.552 -6.497
26 C6 C C6 N Y N 0 1.128 -0.781 7.655
27 O41 O O41 N N N 0 -2.482 -0.14 -2.529
28 O42 O O42 N N N 0 -2.482 0.135 2.529
29 H2 H H2 N N N 0 -2.356 -0.002 0.0
30 H71 H 1H7 N N N 0 0.99 -2.322 9.125
31 H72 H 2H7 N N N 0 1.62 -2.855 7.548
32 H73 H 3H7 N N N 0 2.651 -1.903 8.643
33 H81 H 1H8 N N N 0 0.989 2.324 -9.124
34 H82 H 2H8 N N N 0 1.617 2.857 -7.546
35 H83 H 3H8 N N N 0 2.651 1.907 -8.64
36 H111 H 1H11 N N N 0 -1.889 -0.617 5.053
37 H112 H 2H11 N N N 0 -1.89 1.159 4.956
38 H21 H H21 N N N 0 -0.162 1.793 -6.282
39 H24 H H24 N N N 0 1.495 -2.562 -7.872
40 H30 H H30 N N N 0 -0.157 2.464 6.046
41 H31 H H31 N N N 0 1.489 2.565 7.874
42 H32 H H32 N N N 0 2.313 0.486 8.905
43 H34 H H34 N N N 0 -0.152 -1.794 6.276
44 H5 H H5 N N N 0 2.487 0.002 0.0
45 H10 H H10 N N N 0 0.404 0.197 3.621
46 H16 H H16 N N N 0 0.405 -0.196 -3.621
47 H171 H 1H17 N N N 0 -1.89 0.613 -5.053
48 H172 H 2H17 N N N 0 -1.888 -1.163 -4.956
49 H23 H H23 N N N 0 2.316 -0.482 -8.903
50 H25 H H25 N N N 0 -0.152 -2.465 -6.045



PB3 : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C sing 1.4 N Y
2 C1 N6 C N doub 1.33 N Y
3 C1 C15 C C sing 1.48 N N
4 C2 C3 C C doub 1.4 N Y
5 C2 H2 C H sing 1.08 N N
6 C3 C9 C C sing 1.48 N N
7 C3 N4 C N sing 1.33 N Y
8 N6 C5 N C sing 1.32 N Y
9 C7 C6 C C sing 1.51 N N
10 C7 H71 C H sing 1.09 N N
11 C7 H72 C H sing 1.09 N N
12 C7 H73 C H sing 1.09 N N
13 C8 C4 C C sing 1.51 N N
14 C8 H81 C H sing 1.09 N N
15 C8 H82 C H sing 1.09 N N
16 C8 H83 C H sing 1.09 N N
17 C9 N10 C N sing 1.35 N N
18 C9 O42 C O doub 1.21 N N
19 C11 C12 C C sing 1.51 N N
20 C11 N10 C N sing 1.46 N N
21 C11 H111 C H sing 1.09 N N
22 C11 H112 C H sing 1.09 N N
23 C12 C30 C C doub 1.38 N Y
24 C12 C34 C C sing 1.38 N Y
25 C15 N16 C N sing 1.35 N N
26 C15 O41 C O doub 1.22 N N
27 C21 C18 C C sing 1.38 N Y
28 C21 C4 C C doub 1.38 N Y
29 C21 H21 C H sing 1.08 N N
30 C24 C23 C C doub 1.38 N Y
31 C24 C25 C C sing 1.38 N Y
32 C24 H24 C H sing 1.08 N N
33 C30 C31 C C sing 1.38 N Y
34 C30 H30 C H sing 1.08 N N
35 C31 C32 C C doub 1.38 N Y
36 C31 H31 C H sing 1.08 N N
37 C32 C6 C C sing 1.38 N Y
38 C32 H32 C H sing 1.08 N N
39 C34 C6 C C doub 1.38 N Y
40 C34 H34 C H sing 1.08 N N
41 N4 C5 N C doub 1.32 N Y
42 C5 H5 C H sing 1.08 N N
43 N10 H10 N H sing 0.97 N N
44 N16 C17 N C sing 1.47 N N
45 N16 H16 N H sing 0.97 N N
46 C17 C18 C C sing 1.51 N N
47 C17 H171 C H sing 1.09 N N
48 C17 H172 C H sing 1.09 N N
49 C18 C25 C C doub 1.38 N Y
50 C4 C23 C C sing 1.38 N Y
51 C23 H23 C H sing 1.08 N N
52 C25 H25 C H sing 1.08 N N



PB3 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
PB3 1xuc Open in New Window Bound ligand 2 1