Chemical Components in the PDB

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VRD : Summary

Code

VRD

One-letter code

X

Molecule name

({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid

Synonyms

Varespladib

Systematic names

ProgramVersionName
ACDLabs 12.01 ({3-[amino(oxo)acetyl]-1-benzyl-2-ethyl-1H-indol-4-yl}oxy)acetic acid
OpenEye OEToolkits 2.0.7 2-[2-ethyl-3-oxamoyl-1-(phenylmethyl)indol-4-yl]oxyethanoic acid

Formula

C21 H20 N2 O5

Formal charge

0

Molecular weight

380.394 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 CCc2c(C(C(=O)N)=O)c1c(cccc1n2Cc3ccccc3)OCC(=O)O
SMILES CACTVS 3.385 CCc1n(Cc2ccccc2)c3cccc(OCC(O)=O)c3c1C(=O)C(N)=O
SMILES OpenEye OEToolkits 2.0.7 CCc1c(c2c(n1Cc3ccccc3)cccc2OCC(=O)O)C(=O)C(=O)N
Canonical SMILES CACTVS 3.385 CCc1n(Cc2ccccc2)c3cccc(OCC(O)=O)c3c1C(=O)C(N)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 CCc1c(c2c(n1Cc3ccccc3)cccc2OCC(=O)O)C(=O)C(=O)N

IUPAC InChI

InChI=1S/C21H20N2O5/c1-2-14-19(20(26)21(22)27)18-15(9-6-10-16(18)28-12-17(24)25)23(14)11-13-7-4-3-5-8-13/h3-10H,2,11-12H2,1H3,(H2,22,27)(H,24,25)

IUPAC InChI key

BHLXTPHDSZUFHR-UHFFFAOYSA-N
VRD

wwPDB Information

Atom count

48 (28 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2019-07-25

Last modified at

2021-03-08

Status

Released

Obsoleted

Not Assigned



VRD : Atoms of Molecule

Total Number of Atoms: 48
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C01 C C1 N N N 0 1.535 3.055 -2.338
2 C02 C C2 N N N 0 1.745 2.468 -0.941
3 C03 C C3 N Y N 0 1.076 1.12 -0.857
4 C04 C C4 N Y N 0 -0.256 0.909 -0.551
5 C05 C C5 N Y N 0 -0.457 -0.553 -0.585
6 C06 C C6 N Y N 0 0.79 -1.105 -0.914
7 C08 C C7 N N N 0 3.095 -0.221 -1.422
8 C09 C C8 N Y N 0 3.897 -0.461 -0.169
9 C10 C C9 N Y N 0 4.066 -1.747 0.308
10 C11 C C10 N Y N 0 4.801 -1.967 1.458
11 C12 C C11 N Y N 0 5.368 -0.901 2.13
12 C13 C C12 N Y N 0 5.201 0.386 1.652
13 C14 C C13 N Y N 0 4.47 0.605 0.5
14 C15 C C14 N Y N 0 0.917 -2.486 -1.022
15 C16 C C15 N Y N 0 -0.175 -3.299 -0.807
16 C17 C C16 N Y N 0 -1.408 -2.756 -0.482
17 C18 C C17 N Y N 0 -1.557 -1.385 -0.37
18 C20 C C18 N N N 0 -3.844 -1.767 0.155
19 C21 C C19 N N N 0 -5.095 -0.999 0.497
20 C24 C C20 N N N 0 -1.261 1.927 -0.253
21 C26 C C21 N N N 0 -1.417 2.436 1.14
22 N07 N N1 N Y N 0 1.681 -0.062 -1.074
23 N28 N N2 N N N 0 -2.413 3.295 1.436
24 O19 O O1 N N N 0 -2.766 -0.852 -0.051
25 O22 O O2 N N N 0 -5.066 0.207 0.557
26 O23 O O3 N N N 0 -6.242 -1.656 0.734
27 O25 O O4 N N N 0 -1.97 2.36 -1.141
28 O27 O O5 N N N 0 -0.647 2.077 2.007
29 H1 H H1 N N N 0 0.468 3.089 -2.561
30 H2 H H2 N N N 0 1.946 4.064 -2.374
31 H3 H H3 N N N 0 2.04 2.43 -3.075
32 H4 H H4 N N N 0 2.812 2.356 -0.751
33 H5 H H5 N N N 0 1.311 3.136 -0.197
34 H6 H H6 N N N 0 3.452 0.683 -1.915
35 H7 H H7 N N N 0 3.21 -1.071 -2.095
36 H8 H H8 N N N 0 3.622 -2.581 -0.216
37 H9 H H9 N N N 0 4.932 -2.972 1.831
38 H10 H H10 N N N 0 5.939 -1.072 3.031
39 H11 H H11 N N N 0 5.644 1.219 2.177
40 H12 H H12 N N N 0 4.339 1.61 0.126
41 H13 H H13 N N N 0 1.872 -2.921 -1.275
42 H14 H H14 N N N 0 -0.069 -4.371 -0.892
43 H15 H H15 N N N 0 -2.256 -3.405 -0.316
44 H16 H H16 N N N 0 -3.596 -2.441 0.974
45 H17 H H17 N N N 0 -4.009 -2.345 -0.754
46 H18 H H18 N N N 0 -3.029 3.581 0.743
47 H19 H H19 N N N 0 -2.515 3.626 2.342
48 H20 H H20 N N N 0 -7.018 -1.121 0.949



VRD : Chemical Bonds

Total Number of Bonds: 50
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C12 C13 C C doub 1.38 N Y
2 C12 C11 C C sing 1.38 N Y
3 C13 C14 C C sing 1.38 N Y
4 C11 C10 C C doub 1.38 N Y
5 C14 C09 C C doub 1.38 N Y
6 C10 C09 C C sing 1.38 N Y
7 C09 C08 C C sing 1.51 N N
8 C08 N07 C N sing 1.46 N N
9 C15 C06 C C doub 1.39 N Y
10 C15 C16 C C sing 1.38 N Y
11 N07 C06 N C sing 1.38 N Y
12 N07 C03 N C sing 1.35 N Y
13 C06 C05 C C sing 1.4 N Y
14 C16 C17 C C doub 1.39 N Y
15 C02 C03 C C sing 1.51 N N
16 C02 C01 C C sing 1.53 N N
17 C03 C04 C C doub 1.38 N Y
18 C05 C04 C C sing 1.48 N Y
19 C05 C18 C C doub 1.4 N Y
20 C17 C18 C C sing 1.38 N Y
21 C04 C24 C C sing 1.46 N N
22 C18 O19 C O sing 1.36 N N
23 O25 C24 O C doub 1.22 N N
24 C24 C26 C C sing 1.49 N N
25 C20 O19 C O sing 1.43 N N
26 C20 C21 C C sing 1.51 N N
27 C21 O22 C O doub 1.21 N N
28 C21 O23 C O sing 1.34 N N
29 C26 O27 C O doub 1.21 N N
30 C26 N28 C N sing 1.35 N N
31 C01 H1 C H sing 1.09 N N
32 C01 H2 C H sing 1.09 N N
33 C01 H3 C H sing 1.09 N N
34 C02 H4 C H sing 1.09 N N
35 C02 H5 C H sing 1.09 N N
36 C08 H6 C H sing 1.09 N N
37 C08 H7 C H sing 1.09 N N
38 C10 H8 C H sing 1.08 N N
39 C11 H9 C H sing 1.08 N N
40 C12 H10 C H sing 1.08 N N
41 C13 H11 C H sing 1.08 N N
42 C14 H12 C H sing 1.08 N N
43 C15 H13 C H sing 1.08 N N
44 C16 H14 C H sing 1.08 N N
45 C17 H15 C H sing 1.08 N N
46 C20 H16 C H sing 1.09 N N
47 C20 H17 C H sing 1.09 N N
48 N28 H18 N H sing 0.97 N N
49 N28 H19 N H sing 0.97 N N
50 O23 H20 O H sing 0.97 N N



VRD : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
VRD 6pwh Open in New Window Bound ligand 2 1
VRD 7lye Open in New Window Bound ligand 4 1
VRD 8dnd Open in New Window Bound ligand 3 1