Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

JPH : Summary

Code

JPH

One-letter code

X

Molecule name

2-[2-[4-(2,3-dihydro-1,4-benzodioxin-6-yl)-1,2,3-triazol-1-yl]ethyl]-6-methyl-1~{H}-pyrimidin-4-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 2-[2-[4-(2,3-dihydro-1,4-benzodioxin-6-yl)-1,2,3-triazol-1-yl]ethyl]-6-methyl-1~{H}-pyrimidin-4-one

Formula

C17 H17 N5 O3

Formal charge

0

Molecular weight

339.349 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 CC1=CC(=O)N=C(CCn2cc(nn2)c3ccc4OCCOc4c3)N1
SMILES OpenEye OEToolkits 2.0.7 CC1=CC(=O)N=C(N1)CCn2cc(nn2)c3ccc4c(c3)OCCO4
Canonical SMILES CACTVS 3.385 CC1=CC(=O)N=C(CCn2cc(nn2)c3ccc4OCCOc4c3)N1
Canonical SMILES OpenEye OEToolkits 2.0.7 CC1=CC(=O)N=C(N1)CCn2cc(nn2)c3ccc4c(c3)OCCO4

IUPAC InChI

InChI=1S/C17H17N5O3/c1-11-8-17(23)19-16(18-11)4-5-22-10-13(20-21-22)12-2-3-14-15(9-12)25-7-6-24-14/h2-3,8-10H,4-7H2,1H3,(H,18,19,23)

IUPAC InChI key

HUPUXSMUAITIDA-UHFFFAOYSA-N
JPH

wwPDB Information

Atom count

42 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-03-14

Last modified at

2020-02-14

Status

Released

Obsoleted

Not Assigned



JPH : 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 N1 N N1 N N N 0 4.804 0.853 -0.337
2 N3 N N2 N N N 0 5.378 -1.151 0.668
3 C4 C C1 N N N 0 6.688 -0.786 0.747
4 C5 C C2 N N N 0 7.066 0.424 0.275
5 C6 C C3 N N N 0 6.081 1.271 -0.287
6 CAU C C4 N Y N 0 -3.788 -0.744 -0.394
7 CAT C C5 N Y N 0 -5.102 -0.445 -0.076
8 OAV O O1 N N N 0 -6.078 -1.352 -0.355
9 CAW C C6 N N N 0 -7.331 -1.177 0.315
10 CAX C C7 N N N 0 -7.724 0.303 0.218
11 OAY O O2 N N N 0 -6.698 1.081 0.844
12 CAS C C8 N Y N 0 -5.412 0.773 0.52
13 CAR C C9 N Y N 0 -4.405 1.689 0.793
14 CAQ C C10 N Y N 0 -3.095 1.395 0.476
15 CAP C C11 N Y N 0 -2.778 0.173 -0.114
16 CAM C C12 N Y N 0 -1.368 -0.145 -0.454
17 CAL C C13 N Y N 0 -0.266 0.607 -0.168
18 NAN N N3 N Y N 0 -0.92 -1.236 -1.101
19 NAO N N4 N Y N 0 0.359 -1.157 -1.209
20 NAK N N5 N Y N 0 0.791 -0.074 -0.666
21 CAJ C C14 N N N 0 2.192 0.349 -0.596
22 CAI C C15 N N N 0 3.026 -0.756 0.054
23 C2 C C16 N N N 0 4.467 -0.321 0.127
24 CAA C C17 N N N 0 7.704 -1.72 1.354
25 O6 O O3 N N N 0 6.387 2.37 -0.724
26 H1 H H1 N N N 0 8.099 0.738 0.326
27 H3 H H3 N N N 0 -3.545 -1.69 -0.856
28 H4 H H4 N N N 0 -8.093 -1.792 -0.164
29 H5 H H5 N N N 0 -7.232 -1.464 1.362
30 H6 H H6 N N N 0 -7.816 0.591 -0.83
31 H7 H H7 N N N 0 -8.673 0.466 0.729
32 H8 H H8 N N N 0 -4.649 2.636 1.25
33 H9 H H9 N N N 0 -2.315 2.11 0.689
34 H10 H H10 N N N 0 -0.243 1.554 0.351
35 H11 H H11 N N N 0 2.564 0.541 -1.602
36 H12 H H12 N N N 0 2.267 1.259 -0.001
37 H13 H H13 N N N 0 2.654 -0.948 1.061
38 H14 H H14 N N N 0 2.951 -1.666 -0.541
39 H15 H H15 N N N 0 8.12 -2.359 0.576
40 H16 H H16 N N N 0 8.503 -1.138 1.813
41 H17 H H17 N N N 0 7.222 -2.337 2.112
42 H18 H H18 N N N 0 5.099 -2.017 1.004



JPH : Chemical Bonds

Total Number of Bonds: 45
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAR CAQ C C doub 1.38 N Y
2 CAR CAS C C sing 1.39 N Y
3 CAX OAY C O sing 1.43 N N
4 CAX CAW C C sing 1.53 N N
5 OAY CAS O C sing 1.36 N N
6 CAQ CAP C C sing 1.39 N Y
7 CAS CAT C C doub 1.39 N Y
8 CAP CAM C C sing 1.48 N N
9 CAP CAU C C doub 1.39 N Y
10 CAT CAU C C sing 1.38 N Y
11 CAT OAV C O sing 1.36 N N
12 CAW OAV C O sing 1.43 N N
13 CAM CAL C C doub 1.36 N Y
14 CAM NAN C N sing 1.35 N Y
15 CAL NAK C N sing 1.35 N Y
16 NAN NAO N N doub 1.29 N Y
17 NAK NAO N N sing 1.29 N Y
18 NAK CAJ N C sing 1.47 N N
19 CAJ CAI C C sing 1.53 N N
20 CAI C2 C C sing 1.51 N N
21 N1 C2 N C doub 1.31 N N
22 N1 C6 N C sing 1.34 N N
23 C2 N3 C N sing 1.35 N N
24 O6 C6 O C doub 1.22 N N
25 C6 C5 C C sing 1.42 N N
26 N3 C4 N C sing 1.36 N N
27 C5 C4 C C doub 1.35 N N
28 C4 CAA C C sing 1.51 N N
29 C5 H1 C H sing 1.08 N N
30 CAU H3 C H sing 1.08 N N
31 CAW H4 C H sing 1.09 N N
32 CAW H5 C H sing 1.09 N N
33 CAX H6 C H sing 1.09 N N
34 CAX H7 C H sing 1.09 N N
35 CAR H8 C H sing 1.08 N N
36 CAQ H9 C H sing 1.08 N N
37 CAL H10 C H sing 1.08 N N
38 CAJ H11 C H sing 1.09 N N
39 CAJ H12 C H sing 1.09 N N
40 CAI H13 C H sing 1.09 N N
41 CAI H14 C H sing 1.09 N N
42 CAA H15 C H sing 1.09 N N
43 CAA H16 C H sing 1.09 N N
44 CAA H17 C H sing 1.09 N N
45 N3 H18 N H sing 0.97 N N



JPH : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
JPH 6r1p Open in New Window Bound ligand 1 1