Chemical Components in the PDB

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333 : Summary

Code

333

One-letter code

X

Molecule name

4-(1,3-BENZODIOXOL-5-YLOXY)-2-[4-(1H-IMIDAZOL-1-YL)PHENOXY]PYRIMIDINE

Systematic names

ProgramVersionName
ACDLabs 10.04 4-(1,3-benzodioxol-5-yloxy)-2-[4-(1H-imidazol-1-yl)phenoxy]pyrimidine
OpenEye OEToolkits 1.5.0 4-(1,3-benzodioxol-5-yloxy)-2-(4-imidazol-1-ylphenoxy)pyrimidine

Formula

C20 H14 N4 O4

Formal charge

0

Molecular weight

374.35 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O4c5ccc(Oc3nc(Oc2ccc(n1ccnc1)cc2)ncc3)cc5OC4
SMILES CACTVS 3.341 C1Oc2ccc(Oc3ccnc(Oc4ccc(cc4)n5ccnc5)n3)cc2O1
SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1n2ccnc2)Oc3nccc(n3)Oc4ccc5c(c4)OCO5
Canonical SMILES CACTVS 3.341 C1Oc2ccc(Oc3ccnc(Oc4ccc(cc4)n5ccnc5)n3)cc2O1
Canonical SMILES OpenEye OEToolkits 1.5.0 c1cc(ccc1n2ccnc2)Oc3nccc(n3)Oc4ccc5c(c4)OCO5

IUPAC InChI

InChI=1S/C20H14N4O4/c1-3-15(4-2-14(1)24-10-9-21-12-24)28-20-22-8-7-19(23-20)27-16-5-6-17-18(11-16)26-13-25-17/h1-12H,13H2

IUPAC InChI key

XPXGYINSBORUMM-UHFFFAOYSA-N
333

wwPDB Information

Atom count

42 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2007-02-07

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



333 : Atoms of Molecule

Total Number of Atoms: 42
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C36 C C36 N Y N 0 -1.631 -1.546 -1.186
2 C35 C C35 N Y N 0 -2.54 -2.564 -0.981
3 O39 O O39 N N N 0 -3.361 -3.102 -1.923
4 C38 C C38 N N N 0 -4.06 -4.095 -1.145
5 O37 O O37 N N N 0 -3.648 -4.13 0.237
6 C34 C C34 N Y N 0 -2.704 -3.151 0.252
7 C33 C C33 N Y N 0 -1.968 -2.753 1.35
8 C32 C C32 N Y N 0 -1.041 -1.724 1.169
9 C31 C C31 N Y N 0 -0.873 -1.124 -0.091
10 O28 O O28 N N N 0 0.037 -0.122 -0.244
11 C23 C C23 N Y N 0 1.329 -0.475 -0.595
12 N22 N N22 N Y N 0 1.569 -1.787 -0.754
13 C24 C C24 N Y N 0 2.262 0.518 -0.755
14 C25 C C25 N Y N 0 3.525 0.085 -1.105
15 N26 N N26 N Y N 0 3.849 -1.213 -1.283
16 C21 C C21 N Y N 0 2.838 -2.082 -1.094
17 O17 O O17 N N N 0 3.133 -3.414 -1.268
18 C14 C C14 N Y N 0 2.108 -4.316 -1.078
19 C15 C C15 N Y N 0 1.896 -4.848 0.184
20 C16 C C16 N Y N 0 0.858 -5.76 0.377
21 C13 C C13 N Y N 0 1.308 -4.673 -2.152
22 C12 C C12 N Y N 0 0.27 -5.584 -1.96
23 C11 C C11 N Y N 0 0.045 -6.128 -0.695
24 N3 N N3 N Y N 0 -0.984 -7.031 -0.504
25 C4 C C4 N Y N 0 -1.325 -7.646 0.674
26 C5 C C5 N Y N 0 -2.399 -8.446 0.364
27 NFE N NFE N Y N 0 -2.728 -8.342 -0.964
28 C2 C C2 N Y N 0 -1.861 -7.486 -1.457
29 H36 H H36 N N N 0 -1.509 -1.089 -2.162
30 H381 H 1H38 N N N 0 -3.881 -5.08 -1.589
31 H382 H 2H38 N N N 0 -5.134 -3.88 -1.185
32 H33 H H33 N N N 0 -2.101 -3.217 2.32
33 H32 H H32 N N N 0 -0.445 -1.387 2.014
34 H24 H H24 N N N 0 2.037 1.568 -0.62
35 H25 H H25 N N N 0 4.335 0.79 -1.256
36 H15 H H15 N N N 0 2.525 -4.565 1.024
37 H16 H H16 N N N 0 0.693 -6.175 1.369
38 H13 H H13 N N N 0 1.478 -4.253 -3.14
39 H12 H H12 N N N 0 -0.356 -5.863 -2.804
40 H4 H H4 N N N 0 -0.793 -7.467 1.599
41 H5 H H5 N N N 0 -2.953 -9.092 1.03
42 H2 H H2 N N N 0 -1.817 -7.159 -2.488



333 : Chemical Bonds

Total Number of Bonds: 46
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C36 C31 C C doub 1.4 N Y
2 C36 C35 C C sing 1.38 N Y
3 C36 H36 C H sing 1.08 N N
4 C35 O39 C O sing 1.36 N N
5 C35 C34 C C doub 1.38 N Y
6 O39 C38 O C sing 1.44 N N
7 C38 O37 C O sing 1.44 N N
8 C38 H381 C H sing 1.1 N N
9 C38 H382 C H sing 1.1 N N
10 O37 C34 O C sing 1.36 N N
11 C34 C33 C C sing 1.38 N Y
12 C33 C32 C C doub 1.4 N Y
13 C33 H33 C H sing 1.08 N N
14 C32 C31 C C sing 1.41 N Y
15 C32 H32 C H sing 1.09 N N
16 C31 O28 C O sing 1.36 N N
17 O28 C23 O C sing 1.38 N N
18 C23 C24 C C doub 1.37 N Y
19 C23 N22 C N sing 1.34 N Y
20 N22 C21 N C doub 1.35 N Y
21 C24 C25 C C sing 1.38 N Y
22 C24 H24 C H sing 1.08 N N
23 C25 N26 C N doub 1.35 N Y
24 C25 H25 C H sing 1.08 N N
25 N26 C21 N C sing 1.35 N Y
26 C21 O17 C O sing 1.38 N N
27 O17 C14 O C sing 1.38 N N
28 C14 C15 C C doub 1.39 N Y
29 C14 C13 C C sing 1.39 N Y
30 C15 C16 C C sing 1.4 N Y
31 C15 H15 C H sing 1.09 N N
32 C16 C11 C C doub 1.39 N Y
33 C16 H16 C H sing 1.09 N N
34 C13 C12 C C doub 1.39 N Y
35 C13 H13 C H sing 1.09 N N
36 C12 C11 C C sing 1.4 N Y
37 C12 H12 C H sing 1.09 N N
38 C11 N3 C N sing 1.38 N Y
39 N3 C4 N C sing 1.37 N Y
40 N3 C2 N C sing 1.37 N Y
41 C4 C5 C C doub 1.37 N Y
42 C4 H4 C H sing 1.08 N N
43 C5 NFE C N sing 1.37 N Y
44 C5 H5 C H sing 1.08 N N
45 NFE C2 N C doub 1.31 N Y
46 C2 H2 C H sing 1.08 N N



333 : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
333 2orr Open in New Window Bound ligand 1 1