Chemical Components in the PDB

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X4C : Summary

Code

X4C

One-letter code

X

Molecule name

8-methyl-6-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-a]pyrimidine

Systematic names

ProgramVersionName
ACDLabs 12.01 8-methyl-6-[2-(5-methyl-1-phenyl-1H-benzimidazol-2-yl)ethyl]imidazo[1,5-a]pyrimidine
OpenEye OEToolkits 1.7.6 8-methyl-6-[2-(5-methyl-1-phenyl-benzimidazol-2-yl)ethyl]imidazo[1,5-a]pyrimidine

Formula

C23 H21 N5

Formal charge

0

Molecular weight

367.446 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n2c1cc(ccc1n(c2CCc4nc(c3ncccn34)C)c5ccccc5)C
SMILES CACTVS 3.385 Cc1ccc2n(c(CCc3nc(C)c4ncccn34)nc2c1)c5ccccc5
SMILES OpenEye OEToolkits 1.7.6 Cc1ccc2c(c1)nc(n2c3ccccc3)CCc4nc(c5n4cccn5)C
Canonical SMILES CACTVS 3.385 Cc1ccc2n(c(CCc3nc(C)c4ncccn34)nc2c1)c5ccccc5
Canonical SMILES OpenEye OEToolkits 1.7.6 Cc1ccc2c(c1)nc(n2c3ccccc3)CCc4nc(c5n4cccn5)C

IUPAC InChI

InChI=1S/C23H21N5/c1-16-9-10-20-19(15-16)26-22(28(20)18-7-4-3-5-8-18)12-11-21-25-17(2)23-24-13-6-14-27(21)23/h3-10,13-15H,11-12H2,1-2H3

IUPAC InChI key

VOYXDWSUNQJWTO-UHFFFAOYSA-N
X4C

wwPDB Information

Atom count

49 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2014-03-13

Last modified at

2014-05-30

Status

Released

Obsoleted

Not Assigned



X4C : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C25 C C25 N Y N 0 -0.232 4.103 0.067
2 C24 C C24 N Y N 0 0.14 3.148 -0.861
3 C26 C C26 N Y N 0 -1.158 3.795 1.048
4 C17 C C17 N Y N 0 -5.597 0.069 -0.395
5 C15 C C15 N Y N 0 -4.384 0.71 -0.26
6 C23 C C23 N Y N 0 -0.417 1.884 -0.815
7 C27 C C27 N Y N 0 -1.714 2.532 1.102
8 C12 C C12 N Y N 0 -4.573 -2.051 0.032
9 C16 C C16 N Y N 0 -5.685 -1.309 -0.248
10 C8 C C8 N Y N 0 -3.333 -1.423 0.173
11 C10 C C10 N Y N 0 -3.244 -0.029 0.024
12 C18 C C18 N Y N 0 -1.351 1.574 0.165
13 C9 C C9 N Y N 0 4.392 -2.15 0.124
14 C7 C C7 N Y N 0 4.57 -0.788 0.0
15 C1 C C1 N Y N 0 -1.25 -0.872 0.469
16 C2 C C2 N Y N 0 2.452 -1.297 -0.312
17 C21 C C21 N Y N 0 4.279 1.882 -0.363
18 C14 C C14 N Y N 0 3.186 1.09 -0.462
19 C22 C C22 N Y N 0 5.529 1.308 -0.071
20 C20 C C20 N N N 0 -7.02 -1.992 -0.398
21 C28 C C28 N N N 0 5.466 -3.163 0.43
22 C11 C C11 N N N 0 0.228 -0.983 0.739
23 C13 C C13 N N N 0 0.974 -1.187 -0.582
24 N4 N N4 N Y N 0 -2.081 -1.873 0.443
25 N3 N N3 N Y N 0 3.098 -2.409 -0.069
26 N19 N N19 N Y N 0 5.642 0.013 0.097
27 N5 N N5 N Y N 0 -1.913 0.292 0.217
28 N6 N N6 N Y N 0 3.325 -0.26 -0.28
29 H1 H H1 N N N 0 0.204 5.09 0.029
30 H2 H H2 N N N 0 0.866 3.39 -1.623
31 H3 H H3 N N N 0 -1.446 4.543 1.771
32 H4 H H4 N N N 0 -6.486 0.642 -0.612
33 H5 H H5 N N N 0 -4.322 1.782 -0.375
34 H6 H H6 N N N 0 -0.126 1.139 -1.54
35 H7 H H7 N N N 0 -2.436 2.292 1.868
36 H8 H H8 N N N 0 -4.652 -3.123 0.144
37 H9 H H9 N N N 0 4.191 2.949 -0.503
38 H10 H H10 N N N 0 2.22 1.516 -0.686
39 H11 H H11 N N N 0 6.402 1.937 0.008
40 H12 H H12 N N N 0 -7.168 -2.274 -1.441
41 H13 H H13 N N N 0 -7.044 -2.884 0.227
42 H14 H H14 N N N 0 -7.813 -1.31 -0.091
43 H15 H H15 N N N 0 5.547 -3.292 1.51
44 H16 H H16 N N N 0 5.208 -4.116 -0.031
45 H17 H H17 N N N 0 6.419 -2.813 0.034
46 H18 H H18 N N N 0 0.58 -0.069 1.217
47 H19 H H19 N N N 0 0.415 -1.832 1.396
48 H20 H H20 N N N 0 0.787 -0.338 -1.239
49 H21 H H21 N N N 0 0.622 -2.101 -1.06



X4C : Chemical Bonds

Total Number of Bonds: 53
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C17 C15 C C doub 1.38 N Y
2 C17 C16 C C sing 1.39 N Y
3 C15 C10 C C sing 1.39 N Y
4 C20 C16 C C sing 1.51 N N
5 C26 C25 C C doub 1.38 N Y
6 C26 C27 C C sing 1.38 N Y
7 C25 C24 C C sing 1.38 N Y
8 C16 C12 C C doub 1.37 N Y
9 C27 C18 C C doub 1.39 N Y
10 C24 C23 C C doub 1.38 N Y
11 C10 N5 C N sing 1.38 N Y
12 C10 C8 C C doub 1.4 N Y
13 C18 C23 C C sing 1.39 N Y
14 C18 N5 C N sing 1.4 N N
15 C12 C8 C C sing 1.4 N Y
16 N5 C1 N C sing 1.36 N Y
17 C8 N4 C N sing 1.36 N Y
18 C1 N4 C N doub 1.3 N Y
19 C1 C11 C C sing 1.51 N N
20 C11 C13 C C sing 1.53 N N
21 C21 C14 C C doub 1.35 N Y
22 C21 C22 C C sing 1.41 N Y
23 C14 N6 C N sing 1.37 N Y
24 C13 C2 C C sing 1.51 N N
25 N6 C2 N C sing 1.36 N Y
26 N6 C7 N C sing 1.38 N Y
27 C22 N19 C N doub 1.31 N Y
28 C2 N3 C N doub 1.31 N Y
29 C7 N19 C N sing 1.34 N Y
30 C7 C9 C C doub 1.38 N Y
31 N3 C9 N C sing 1.33 N Y
32 C9 C28 C C sing 1.51 N N
33 C25 H1 C H sing 1.08 N N
34 C24 H2 C H sing 1.08 N N
35 C26 H3 C H sing 1.08 N N
36 C17 H4 C H sing 1.08 N N
37 C15 H5 C H sing 1.08 N N
38 C23 H6 C H sing 1.08 N N
39 C27 H7 C H sing 1.08 N N
40 C12 H8 C H sing 1.08 N N
41 C21 H9 C H sing 1.08 N N
42 C14 H10 C H sing 1.08 N N
43 C22 H11 C H sing 1.08 N N
44 C20 H12 C H sing 1.09 N N
45 C20 H13 C H sing 1.09 N N
46 C20 H14 C H sing 1.09 N N
47 C28 H15 C H sing 1.09 N N
48 C28 H16 C H sing 1.09 N N
49 C28 H17 C H sing 1.09 N N
50 C11 H18 C H sing 1.09 N N
51 C11 H19 C H sing 1.09 N N
52 C13 H20 C H sing 1.09 N N
53 C13 H21 C H sing 1.09 N N



X4C : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
X4C 3ws8 Open in New Window Bound ligand 2 1