Chemical Components in the PDB

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SRK : Summary

Code

SRK

One-letter code

X

Molecule name

4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoic acid

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 4-(2,3-dihydroindol-1-yl)-4-oxidanylidene-butanoic acid

Formula

C12 H13 N O3

Formal charge

0

Molecular weight

219.237 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 OC(=O)CCC(=O)N1CCc2ccccc12
SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)CCN2C(=O)CCC(=O)O
Canonical SMILES CACTVS 3.385 OC(=O)CCC(=O)N1CCc2ccccc12
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)CCN2C(=O)CCC(=O)O

IUPAC InChI

InChI=1S/C12H13NO3/c14-11(5-6-12(15)16)13-8-7-9-3-1-2-4-10(9)13/h1-4H,5-8H2,(H,15,16)

IUPAC InChI key

SWNRXQYQTQVWKA-UHFFFAOYSA-N
SRK

wwPDB Information

Atom count

29 (16 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-11-30

Last modified at

2021-07-30

Status

Released

Obsoleted

Not Assigned



SRK : Atoms of Molecule

Total Number of Atoms: 29
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C02 C C1 N N N 0 3.751 -0.561 -0.002
2 C04 C C2 N N N 0 2.828 0.631 -0.001
3 C05 C C3 N N N 0 1.375 0.15 -0.001
4 C06 C C4 N N N 0 0.453 1.342 -0.001
5 C09 C C5 N N N 0 -1.877 2.237 0.0
6 C10 C C6 N N N 0 -3.24 1.526 0.001
7 C11 C C7 N Y N 0 -2.902 0.052 0.001
8 C12 C C8 N Y N 0 -3.715 -1.065 0.001
9 C13 C C9 N Y N 0 -3.158 -2.33 0.0
10 C14 C C10 N Y N 0 -1.783 -2.476 -0.001
11 C15 C C11 N Y N 0 -0.967 -1.364 0.0
12 C16 C C12 N Y N 0 -1.523 -0.083 0.0
13 N08 N N1 N N N 0 -0.883 1.16 0.0
14 O01 O O1 N N N 0 5.081 -0.38 0.004
15 O03 O O2 N N N 0 3.293 -1.679 -0.001
16 O07 O O3 N N N 0 0.912 2.465 -0.001
17 H1 H H1 N N N 0 3.012 1.232 0.889
18 H2 H H2 N N N 0 3.011 1.232 -0.891
19 H3 H H3 N N N 0 1.191 -0.451 -0.891
20 H4 H H4 N N N 0 1.192 -0.451 0.889
21 H5 H H5 N N N 0 -1.771 2.85 -0.895
22 H6 H H6 N N N 0 -1.769 2.851 0.894
23 H7 H H7 N N N 0 -3.805 1.786 0.896
24 H8 H H8 N N N 0 -3.805 1.786 -0.894
25 H9 H H9 N N N 0 -4.789 -0.949 0.001
26 H10 H H10 N N N 0 -3.795 -3.202 0.0
27 H11 H H11 N N N 0 -1.346 -3.463 -0.001
28 H12 H H12 N N N 0 0.106 -1.485 0.0
29 H13 H H13 N N N 0 5.632 -1.174 0.007



SRK : Chemical Bonds

Total Number of Bonds: 30
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C10 C09 C C sing 1.54 N N
2 C10 C11 C C sing 1.51 N N
3 C09 N08 C N sing 1.47 N N
4 C05 C04 C C sing 1.53 N N
5 C05 C06 C C sing 1.51 N N
6 C04 C02 C C sing 1.51 N N
7 N08 C06 N C sing 1.35 N N
8 N08 C16 N C sing 1.4 N N
9 C06 O07 C O doub 1.21 N N
10 C11 C16 C C doub 1.39 N Y
11 C11 C12 C C sing 1.38 N Y
12 C16 C15 C C sing 1.4 N Y
13 C12 C13 C C doub 1.38 N Y
14 C02 O03 C O doub 1.21 N N
15 C02 O01 C O sing 1.34 N N
16 C13 C14 C C sing 1.38 N Y
17 C15 C14 C C doub 1.38 N Y
18 C04 H1 C H sing 1.09 N N
19 C04 H2 C H sing 1.09 N N
20 C05 H3 C H sing 1.09 N N
21 C05 H4 C H sing 1.09 N N
22 C09 H5 C H sing 1.09 N N
23 C09 H6 C H sing 1.09 N N
24 C10 H7 C H sing 1.09 N N
25 C10 H8 C H sing 1.09 N N
26 C12 H9 C H sing 1.08 N N
27 C13 H10 C H sing 1.08 N N
28 C14 H11 C H sing 1.08 N N
29 C15 H12 C H sing 1.08 N N
30 O01 H13 O H sing 0.97 N N



SRK : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
SRK 7b37 Open in New Window Bound ligand 1 1
SRK 7b3f Open in New Window Bound ligand 1 1