Chemical Components in the PDB

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R0S : Summary

Code

R0S

One-letter code

X

Molecule name

4-(5-chloro-2-{[1-(3,4-dimethoxyphenyl)-2-oxo-1,2-dihydro-3H-imidazo[4,5-c]pyridin-3-yl]methyl}-1H-indol-1-yl)butanenitrile

Systematic names

ProgramVersionName
ACDLabs 12.01 4-(5-chloro-2-{[1-(3,4-dimethoxyphenyl)-2-oxo-1,2-dihydro-3H-imidazo[4,5-c]pyridin-3-yl]methyl}-1H-indol-1-yl)butanenitrile
OpenEye OEToolkits 2.0.7 4-[5-chloranyl-2-[[1-(3,4-dimethoxyphenyl)-2-oxidanylidene-imidazo[4,5-c]pyridin-3-yl]methyl]indol-1-yl]butanenitrile

Formula

C27 H24 Cl N5 O3

Formal charge

0

Molecular weight

501.964 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 COc5c(ccc(N4C(N(Cc2cc1c(ccc(Cl)c1)n2CCCC#N)c3cnccc34)=O)c5)OC
SMILES CACTVS 3.385 COc1ccc(cc1OC)N2C(=O)N(Cc3cc4cc(Cl)ccc4n3CCCC#N)c5cnccc25
SMILES OpenEye OEToolkits 2.0.7 COc1ccc(cc1OC)N2c3ccncc3N(C2=O)Cc4cc5cc(ccc5n4CCCC#N)Cl
Canonical SMILES CACTVS 3.385 COc1ccc(cc1OC)N2C(=O)N(Cc3cc4cc(Cl)ccc4n3CCCC#N)c5cnccc25
Canonical SMILES OpenEye OEToolkits 2.0.7 COc1ccc(cc1OC)N2c3ccncc3N(C2=O)Cc4cc5cc(ccc5n4CCCC#N)Cl

IUPAC InChI

InChI=1S/C27H24ClN5O3/c1-35-25-8-6-20(15-26(25)36-2)33-23-9-11-30-16-24(23)32(27(33)34)17-21-14-18-13-19(28)5-7-22(18)31(21)12-4-3-10-29/h5-9,11,13-16H,3-4,12,17H2,1-2H3

IUPAC InChI key

BVLCQPKSGBJPGE-UHFFFAOYSA-N
R0S

wwPDB Information

Atom count

60 (36 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-01-21

Last modified at

2020-05-22

Status

Released

Obsoleted

Not Assigned



R0S : Atoms of Molecule

Total Number of Atoms: 60
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C10 C C1 N N N 0 2.99 -0.579 -3.853
2 C15 C C2 N N N 0 -1.056 0.679 2.214
3 C17 C C3 N Y N 0 -1.922 -1.094 0.633
4 C20 C C4 N Y N 0 -4.76 -2.16 -1.702
5 C22 C C5 N Y N 0 -5.551 -1.037 -1.492
6 C24 C C6 N Y N 0 -3.92 -0.146 0.02
7 C26 C C7 N N N 0 -3.727 1.962 1.393
8 C28 C C8 N N N 0 -3.903 4.399 0.872
9 C01 C C9 N N N 0 7.856 1.12 -1.646
10 C03 C C10 N Y N 0 5.572 0.478 -1.471
11 C04 C C11 N Y N 0 5.673 0.703 -0.108
12 C05 C C12 N Y N 0 4.575 0.506 0.709
13 C06 C C13 N Y N 0 3.371 0.082 0.166
14 C07 C C14 N Y N 0 3.266 -0.144 -1.2
15 C08 C C15 N Y N 0 4.365 0.054 -2.019
16 C12 C C16 N N N 0 1.129 0.617 0.992
17 C16 C C17 N Y N 0 -2.059 0.085 1.26
18 C18 C C18 N Y N 0 -3.118 -1.282 -0.192
19 C19 C C19 N Y N 0 -3.549 -2.288 -1.059
20 C23 C C20 N Y N 0 -5.139 -0.037 -0.64
21 C27 C C21 N N N 0 -3.311 3.064 0.417
22 C29 C C22 N N N 0 -3.584 5.44 -0.118
23 C31 C C23 N Y N 0 0.874 -0.943 2.552
24 C32 C C24 N Y N 0 0.487 -1.808 3.56
25 C34 C C25 N Y N 0 2.49 -2.954 3.425
26 C35 C C26 N Y N 0 2.951 -2.134 2.414
27 C36 C C27 N Y N 0 2.134 -1.105 1.962
28 N11 N N1 N N N 0 2.258 -0.117 0.997
29 N14 N N2 N N N 0 0.275 0.143 1.92
30 N25 N N3 N Y N 0 -3.245 0.668 0.903
31 N30 N N4 N N N 0 -3.338 6.244 -0.882
32 N33 N N5 N Y N 0 1.296 -2.772 3.959
33 O02 O O1 N N N 0 6.652 0.678 -2.275
34 O09 O O2 N N N 0 4.265 -0.167 -3.357
35 O13 O O3 N N N 0 0.915 1.569 0.264
36 CL21 CL CL1 N N N 0 -5.301 -3.408 -2.781
37 H1 H H1 N N N 0 2.721 -1.538 -3.411
38 H2 H H2 N N N 0 2.24 0.167 -3.59
39 H3 H H3 N N N 0 3.037 -0.679 -4.938
40 H4 H H4 N N N 0 -1.044 1.763 2.101
41 H5 H H5 N N N 0 -1.333 0.424 3.237
42 H6 H H6 N N N 0 -1.087 -1.773 0.718
43 H7 H H7 N N N 0 -6.499 -0.948 -2.003
44 H8 H H8 N N N 0 -3.296 2.163 2.373
45 H9 H H9 N N N 0 -4.814 1.938 1.472
46 H10 H H10 N N N 0 -4.985 4.304 0.964
47 H11 H H11 N N N 0 -3.479 4.674 1.838
48 H12 H H12 N N N 0 8.636 1.24 -2.398
49 H13 H H13 N N N 0 7.679 2.075 -1.151
50 H14 H H14 N N N 0 8.173 0.382 -0.908
51 H15 H H15 N N N 0 6.609 1.032 0.317
52 H16 H H16 N N N 0 4.656 0.681 1.772
53 H17 H H17 N N N 0 2.329 -0.474 -1.623
54 H18 H H18 N N N 0 -2.937 -3.162 -1.224
55 H19 H H19 N N N 0 -5.762 0.832 -0.485
56 H20 H H20 N N N 0 -2.224 3.137 0.394
57 H21 H H21 N N N 0 -3.68 2.824 -0.581
58 H22 H H22 N N N 0 -0.481 -1.693 4.023
59 H23 H H23 N N N 0 3.116 -3.757 3.785
60 H24 H H24 N N N 0 3.929 -2.289 1.984



R0S : Chemical Bonds

Total Number of Bonds: 64
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O09 C10 O C sing 1.43 N N
2 O09 C08 O C sing 1.36 N N
3 C01 O02 C O sing 1.43 N N
4 C08 C07 C C doub 1.38 N Y
5 C08 C03 C C sing 1.39 N Y
6 O02 C03 O C sing 1.36 N N
7 C07 C06 C C sing 1.39 N Y
8 O13 C12 O C doub 1.22 N N
9 C03 C04 C C doub 1.39 N Y
10 C12 N11 C N sing 1.35 N N
11 C12 N14 C N sing 1.35 N N
12 C06 N11 C N sing 1.4 N N
13 C06 C05 C C doub 1.39 N Y
14 C28 C29 C C sing 1.47 N N
15 C28 C27 C C sing 1.53 N N
16 C04 C05 C C sing 1.38 N Y
17 C26 C27 C C sing 1.53 N N
18 C26 N25 C N sing 1.47 N N
19 N11 C36 N C sing 1.39 N N
20 C15 N14 C N sing 1.46 N N
21 C15 C16 C C sing 1.51 N N
22 C29 N30 C N trip 1.14 N N
23 N14 C31 N C sing 1.39 N N
24 N25 C16 N C sing 1.37 N Y
25 N25 C24 N C sing 1.38 N Y
26 C16 C17 C C doub 1.34 N Y
27 C36 C31 C C doub 1.4 N Y
28 C36 C35 C C sing 1.39 N Y
29 C31 C32 C C sing 1.38 N Y
30 C24 C23 C C doub 1.39 N Y
31 C24 C18 C C sing 1.41 N Y
32 C17 C18 C C sing 1.47 N Y
33 C35 C34 C C doub 1.38 N Y
34 C23 C22 C C sing 1.38 N Y
35 C32 N33 C N doub 1.32 N Y
36 C18 C19 C C doub 1.4 N Y
37 C34 N33 C N sing 1.32 N Y
38 C22 C20 C C doub 1.39 N Y
39 C19 C20 C C sing 1.38 N Y
40 C20 CL21 C CL sing 1.74 N N
41 C10 H1 C H sing 1.09 N N
42 C10 H2 C H sing 1.09 N N
43 C10 H3 C H sing 1.09 N N
44 C15 H4 C H sing 1.09 N N
45 C15 H5 C H sing 1.09 N N
46 C17 H6 C H sing 1.08 N N
47 C22 H7 C H sing 1.08 N N
48 C26 H8 C H sing 1.09 N N
49 C26 H9 C H sing 1.09 N N
50 C28 H10 C H sing 1.09 N N
51 C28 H11 C H sing 1.09 N N
52 C01 H12 C H sing 1.09 N N
53 C01 H13 C H sing 1.09 N N
54 C01 H14 C H sing 1.09 N N
55 C04 H15 C H sing 1.08 N N
56 C05 H16 C H sing 1.08 N N
57 C07 H17 C H sing 1.08 N N
58 C19 H18 C H sing 1.08 N N
59 C23 H19 C H sing 1.08 N N
60 C27 H20 C H sing 1.09 N N
61 C27 H21 C H sing 1.09 N N
62 C32 H22 C H sing 1.08 N N
63 C34 H23 C H sing 1.08 N N
64 C35 H24 C H sing 1.08 N N



R0S : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
R0S 6vke Open in New Window Bound ligand 1 1