Chemical Components in the PDB

pdbe.org/chem
wwPDB
EMDataBank
spacer

E5R : Summary

Code

E5R

One-letter code

X

Molecule name

(3R)-3-[[(3R)-3-methylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (3~{R})-3-[[(3~{R})-3-methylpiperidin-1-yl]methyl]-6,8-bis(oxidanyl)-3,4-dihydroisochromen-1-one

Formula

C16 H21 N O4

Formal charge

0

Molecular weight

291.342 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH]1CCCN(C1)C[CH]2Cc3cc(O)cc(O)c3C(=O)O2
SMILES OpenEye OEToolkits 2.0.7 CC1CCCN(C1)CC2Cc3cc(cc(c3C(=O)O2)O)O
Canonical SMILES CACTVS 3.385 C[C@@H]1CCCN(C1)C[C@H]2Cc3cc(O)cc(O)c3C(=O)O2
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@@H]1CCCN(C1)C[C@H]2Cc3cc(cc(c3C(=O)O2)O)O

IUPAC InChI

InChI=1S/C16H21NO4/c1-10-3-2-4-17(8-10)9-13-6-11-5-12(18)7-14(19)15(11)16(20)21-13/h5,7,10,13,18-19H,2-4,6,8-9H2,1H3/t10-,13-/m1/s1

IUPAC InChI key

ZNIKUZOBPQNYBK-ZWNOBZJWSA-N
E5R

wwPDB Information

Atom count

42 (21 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-10-21

Last modified at

2021-05-14

Status

Released

Obsoleted

Not Assigned



E5R : 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 N N N1 N N N 0 2.77 0.542 -0.505
2 C C C1 N Y N 0 -3.38 -1.172 -0.021
3 O O O1 N N N 0 -3.424 -2.521 -0.159
4 C12 C C5 N N N 0 4.611 -0.771 2.542
5 C1 C C2 N Y N 0 -4.519 -0.47 0.334
6 C10 C C3 N N N 0 5.455 -0.195 0.26
7 C11 C C4 R N N 0 4.231 -0.641 1.066
8 C13 C C6 N N N 0 3.12 0.401 0.914
9 C14 C C7 N Y N 0 -2.179 -0.481 -0.232
10 C15 C C8 N N N 0 -0.952 -1.213 -0.6
11 C2 C C9 N Y N 0 -4.466 0.909 0.478
12 C3 C C10 N Y N 0 -3.274 1.594 0.266
13 C4 C C11 N Y N 0 -2.133 0.909 -0.089
14 C5 C C12 N N N 0 -0.85 1.661 -0.326
15 C6 C C13 R N N 0 0.349 0.722 -0.186
16 C7 C C14 N N N 0 1.613 1.431 -0.676
17 C8 C C15 N N N 0 3.917 1.014 -1.291
18 O2 O O3 N N N 0 0.119 -0.474 -0.987
19 C9 C C16 N N N 0 5.052 -0.009 -1.205
20 O1 O O2 N N N 0 -5.584 1.594 0.827
21 O3 O O4 N N N 0 -0.902 -2.427 -0.559
22 H2 H H2 N N N 0 -3.645 -2.818 -1.052
23 H3 H H3 N N N 0 -5.449 -0.995 0.498
24 H4 H H4 N N N 0 5.829 0.748 0.658
25 H5 H H5 N N N 0 6.234 -0.955 0.331
26 H6 H H6 N N N 0 3.881 -1.603 0.694
27 H7 H H7 N N N 0 4.96 0.193 2.914
28 H8 H H8 N N N 0 3.74 -1.088 3.115
29 H9 H H9 N N N 0 5.405 -1.51 2.649
30 H10 H H10 N N N 0 3.467 1.36 1.3
31 H11 H H11 N N N 0 2.243 0.08 1.475
32 H12 H H12 N N N 0 -3.243 2.668 0.38
33 H13 H H13 N N N 0 -0.86 2.086 -1.33
34 H14 H H14 N N N 0 -0.764 2.467 0.403
35 H15 H H15 N N N 0 0.471 0.442 0.861
36 H16 H H16 N N N 0 1.766 2.342 -0.097
37 H17 H H17 N N N 0 1.502 1.684 -1.73
38 H18 H H18 N N N 0 3.618 1.138 -2.332
39 H19 H H19 N N N 0 4.259 1.97 -0.895
40 H20 H H20 N N N 0 5.908 0.349 -1.776
41 H21 H H21 N N N 0 4.714 -0.962 -1.613
42 H22 H H22 N N N 0 -5.701 1.695 1.782



E5R : Chemical Bonds

Total Number of Bonds: 44
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O C O C sing 1.36 N N
2 O3 C15 O C doub 1.22 N N
3 C C1 C C doub 1.38 N Y
4 C C14 C C sing 1.4 N Y
5 C1 C2 C C sing 1.39 N Y
6 C15 C14 C C sing 1.48 N N
7 C15 O2 C O sing 1.36 N N
8 C14 C4 C C doub 1.4 N Y
9 C2 O1 C O sing 1.36 N N
10 C2 C3 C C doub 1.39 N Y
11 O2 C6 O C sing 1.46 N N
12 C4 C3 C C sing 1.38 N Y
13 C4 C5 C C sing 1.51 N N
14 C5 C6 C C sing 1.53 N N
15 C6 C7 C C sing 1.53 N N
16 C7 N C N sing 1.47 N N
17 N C8 N C sing 1.47 N N
18 N C13 N C sing 1.47 N N
19 C8 C9 C C sing 1.53 N N
20 C9 C10 C C sing 1.53 N N
21 C13 C11 C C sing 1.53 N N
22 C11 C10 C C sing 1.53 N N
23 C11 C12 C C sing 1.53 N N
24 O H2 O H sing 0.97 N N
25 C1 H3 C H sing 1.08 N N
26 C10 H4 C H sing 1.09 N N
27 C10 H5 C H sing 1.09 N N
28 C11 H6 C H sing 1.09 N N
29 C12 H7 C H sing 1.09 N N
30 C12 H8 C H sing 1.09 N N
31 C12 H9 C H sing 1.09 N N
32 C13 H10 C H sing 1.09 N N
33 C13 H11 C H sing 1.09 N N
34 C3 H12 C H sing 1.08 N N
35 C5 H13 C H sing 1.09 N N
36 C5 H14 C H sing 1.09 N N
37 C6 H15 C H sing 1.09 N N
38 C7 H16 C H sing 1.09 N N
39 C7 H17 C H sing 1.09 N N
40 C8 H18 C H sing 1.09 N N
41 C8 H19 C H sing 1.09 N N
42 C9 H20 C H sing 1.09 N N
43 C9 H21 C H sing 1.09 N N
44 O1 H22 O H sing 0.97 N N



E5R : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
E5R 6l4q Open in New Window Bound ligand 2 1