Chemical Components in the PDB

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JDE : Summary

Code

JDE

One-letter code

X

Molecule name

(3-methoxy-5-pyridin-3-yl-phenyl)methyl 1~{H}-pyrazole-4-carboxylate

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (3-methoxy-5-pyridin-3-yl-phenyl)methyl 1~{H}-pyrazole-4-carboxylate

Formula

C17 H15 N3 O3

Formal charge

0

Molecular weight

309.319 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 COc1cc(COC(=O)c2c[nH]nc2)cc(c1)c3cccnc3
SMILES OpenEye OEToolkits 2.0.7 COc1cc(cc(c1)c2cccnc2)COC(=O)c3c[nH]nc3
Canonical SMILES CACTVS 3.385 COc1cc(COC(=O)c2c[nH]nc2)cc(c1)c3cccnc3
Canonical SMILES OpenEye OEToolkits 2.0.7 COc1cc(cc(c1)c2cccnc2)COC(=O)c3c[nH]nc3

IUPAC InChI

InChI=1S/C17H15N3O3/c1-22-16-6-12(11-23-17(21)15-9-19-20-10-15)5-14(7-16)13-3-2-4-18-8-13/h2-10H,11H2,1H3,(H,19,20)

IUPAC InChI key

JWEGKKOSKAIWMV-UHFFFAOYSA-N
JDE

wwPDB Information

Atom count

38 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-02-19

Last modified at

2019-09-13

Status

Released

Obsoleted

Not Assigned



JDE : Atoms of Molecule

Total Number of Atoms: 38
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N Y N 0 4.25 -0.524 -1.532
2 N12 N N1 N Y N 0 6.345 -1.017 -1.075
3 C13 C C2 N Y N 0 5.772 -0.748 0.109
4 C15 C C3 N Y N 0 -1.026 -0.171 0.755
5 C17 C C4 N Y N 0 -3.252 -1.01 0.007
6 C20 C C5 N Y N 0 -5.002 -3.077 -0.282
7 C21 C C6 N Y N 0 -5.383 -1.818 -0.708
8 C22 C C7 N Y N 0 -4.501 -0.76 -0.567
9 C01 C C8 N N N 0 -3.263 3.868 -1.036
10 O02 O O1 N N N 0 -1.975 3.667 -0.449
11 C03 C C9 N Y N 0 -1.666 2.402 -0.059
12 C04 C C10 N Y N 0 -0.432 2.136 0.518
13 C05 C C11 N Y N 0 -0.114 0.852 0.917
14 C06 C C12 N N N 0 1.233 0.568 1.532
15 O07 O O2 N N N 0 2.178 0.217 0.486
16 C08 C C13 N N N 0 3.437 -0.068 0.871
17 C09 C C14 N Y N 0 4.449 -0.433 -0.135
18 N11 N N2 N Y N 0 5.382 -0.872 -2.079
19 O14 O O3 N N N 0 3.738 -0.025 2.047
20 C16 C C15 N Y N 0 -2.269 0.088 0.182
21 C18 C C16 N Y N 0 -2.946 -2.306 0.417
22 N19 N N3 N Y N 0 -3.817 -3.282 0.262
23 H3 H H3 N N N 0 6.255 -0.774 1.074
24 C23 C C17 N Y N 0 -2.587 1.382 -0.226
25 H1 H H1 N N N 0 3.322 -0.343 -2.054
26 H2 H H2 N N N 0 7.272 -1.27 -1.211
27 H4 H H4 N N N 0 -0.775 -1.174 1.068
28 H5 H H5 N N N 0 -5.687 -3.905 -0.39
29 H7 H H7 N N N 0 -4.773 0.234 -0.891
30 H6 H H6 N N N 0 -6.357 -1.662 -1.148
31 H8 H H8 N N N 0 -4.036 3.585 -0.321
32 H9 H H9 N N N 0 -3.381 4.919 -1.301
33 H10 H H10 N N N 0 -3.354 3.255 -1.932
34 H14 H H14 N N N 0 -1.986 -2.512 0.866
35 H11 H H11 N N N 0 0.282 2.935 0.656
36 H12 H H12 N N N 0 1.586 1.454 2.058
37 H13 H H13 N N N 0 1.144 -0.261 2.234
38 H15 H H15 N N N 0 -3.548 1.587 -0.674



JDE : Chemical Bonds

Total Number of Bonds: 40
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 N19 C18 N C doub 1.32 N Y
2 N19 C20 N C sing 1.32 N Y
3 C18 C17 C C sing 1.39 N Y
4 O02 C01 O C sing 1.43 N N
5 O02 C03 O C sing 1.36 N N
6 C20 C21 C C doub 1.38 N Y
7 C23 C03 C C doub 1.38 N Y
8 C23 C16 C C sing 1.39 N Y
9 C03 C04 C C sing 1.39 N Y
10 C17 C16 C C sing 1.48 N N
11 C17 C22 C C doub 1.4 N Y
12 C16 C15 C C doub 1.39 N Y
13 C21 C22 C C sing 1.38 N Y
14 C04 C05 C C doub 1.38 N Y
15 C15 C05 C C sing 1.38 N Y
16 C05 C06 C C sing 1.51 N N
17 C06 O07 C O sing 1.45 N N
18 O07 C08 O C sing 1.35 N N
19 C10 C09 C C sing 1.41 N Y
20 C10 N11 C N doub 1.3 N Y
21 C08 C09 C C sing 1.47 N N
22 C08 O14 C O doub 1.21 N N
23 C09 C13 C C doub 1.38 N Y
24 N11 N12 N N sing 1.4 N Y
25 C13 N12 C N sing 1.34 N Y
26 C10 H1 C H sing 1.08 N N
27 N12 H2 N H sing 0.97 N N
28 C13 H3 C H sing 1.08 N N
29 C15 H4 C H sing 1.08 N N
30 C20 H5 C H sing 1.08 N N
31 C21 H6 C H sing 1.08 N N
32 C22 H7 C H sing 1.08 N N
33 C01 H8 C H sing 1.09 N N
34 C01 H9 C H sing 1.09 N N
35 C01 H10 C H sing 1.09 N N
36 C04 H11 C H sing 1.08 N N
37 C06 H12 C H sing 1.09 N N
38 C06 H13 C H sing 1.09 N N
39 C18 H14 C H sing 1.08 N N
40 C23 H15 C H sing 1.08 N N



JDE : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
JDE 6qqq Open in New Window Bound ligand 2 1