Chemical Components in the PDB

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RZX : Summary

Code

RZX

One-letter code

X

Molecule name

2-[(R)-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfinyl]-1H-benzimidazole

Systematic names

ProgramVersionName
ACDLabs 12.01 2-[(R)-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfinyl]-1H-benzimidazole
OpenEye OEToolkits 1.7.0 2-[(R)-[4-(3-methoxypropoxy)-3-methyl-pyridin-2-yl]methylsulfinyl]-1H-benzimidazole

Formula

C18 H21 N3 O3 S

Formal charge

0

Molecular weight

359.443 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=S(c2nc1ccccc1n2)Cc3nccc(OCCCOC)c3C
SMILES CACTVS 3.370 COCCCOc1ccnc(C[S](=O)c2[nH]c3ccccc3n2)c1C
SMILES OpenEye OEToolkits 1.7.0 Cc1c(ccnc1CS(=O)c2[nH]c3ccccc3n2)OCCCOC
Canonical SMILES CACTVS 3.370 COCCCOc1ccnc(C[S@@](=O)c2[nH]c3ccccc3n2)c1C
Canonical SMILES OpenEye OEToolkits 1.7.0 Cc1c(ccnc1C[S@@](=O)c2[nH]c3ccccc3n2)OCCCOC

IUPAC InChI

InChI=1S/C18H21N3O3S/c1-13-16(19-9-8-17(13)24-11-5-10-23-2)12-25(22)18-20-14-6-3-4-7-15(14)21-18/h3-4,6-9H,5,10-12H2,1-2H3,(H,20,21)/t25-/m1/s1

IUPAC InChI key

YREYEVIYCVEVJK-RUZDIDTESA-N
RZX

wwPDB Information

Atom count

46 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-11-09

Last modified at

2021-03-01

Status

Released

Obsoleted

Not Assigned



RZX : Atoms of Molecule

Total Number of Atoms: 46
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C1 C C1 N Y N 0 6.09 2.078 0.376
2 C2 C C2 N Y N 0 5.159 1.094 0.036
3 C3 C C3 N Y N 0 5.573 -0.246 -0.059
4 C4 C C4 N Y N 0 6.898 -0.578 0.186
5 C5 C C5 N Y N 0 7.799 0.41 0.521
6 C6 C C6 N Y N 0 7.39 1.733 0.614
7 N7 N N7 N Y N 0 4.449 -0.969 -0.405
8 C8 C C8 N Y N 0 3.417 -0.087 -0.51
9 N9 N N9 N Y N 0 3.832 1.119 -0.252
10 S10 S S10 R N N 0 1.762 -0.516 -0.932
11 C11 C C11 N N N 0 1.003 -0.853 0.68
12 C12 C C12 N Y N 0 -0.44 -1.241 0.486
13 N13 N N13 N Y N 0 -0.757 -2.51 0.316
14 C14 C C14 N Y N 0 -2.006 -2.9 0.142
15 C15 C C15 N Y N 0 -3.037 -1.984 0.13
16 C16 C C16 N Y N 0 -2.745 -0.633 0.306
17 C17 C C17 N Y N 0 -1.415 -0.264 0.492
18 O18 O O18 N N N 0 1.241 0.697 -1.457
19 O19 O O19 N N N 0 -3.732 0.299 0.301
20 C20 C C20 N N N 0 -5.067 -0.171 0.108
21 C21 C C21 N N N 0 -6.034 1.014 0.132
22 C22 C C22 N N N 0 -7.464 0.51 -0.074
23 O23 O O23 N N N 0 -8.367 1.618 -0.051
24 C24 C C24 N N N 0 -9.737 1.255 -0.236
25 C25 C C25 N N N 0 -1.045 1.183 0.693
26 H1 H H1 N N N 0 5.783 3.111 0.447
27 HN7 H HN7 N N N 0 4.402 -1.927 -0.548
28 H4 H H4 N N N 0 7.221 -1.606 0.115
29 H5 H H5 N N N 0 8.831 0.153 0.712
30 H6 H H6 N N N 0 8.107 2.497 0.877
31 H11 H H11 N N N 0 1.535 -1.669 1.169
32 H11A H H11A N N N 0 1.058 0.041 1.302
33 H14 H H14 N N N 0 -2.223 -3.949 0.006
34 H15 H H15 N N N 0 -4.057 -2.309 -0.013
35 H20 H H20 N N N 0 -5.139 -0.679 -0.854
36 H20A H H20A N N N 0 -5.326 -0.868 0.906
37 H21 H H21 N N N 0 -5.963 1.522 1.094
38 H21A H H21A N N N 0 -5.775 1.71 -0.666
39 H22 H H22 N N N 0 -7.536 0.003 -1.036
40 H22A H H22A N N N 0 -7.723 -0.186 0.725
41 H24 H H24 N N N 0 -9.855 0.762 -1.201
42 H24A H H24A N N N 0 -10.042 0.574 0.559
43 H24B H H24B N N N 0 -10.357 2.15 -0.206
44 H25 H H25 N N N 0 -0.849 1.645 -0.275
45 H25A H H25A N N N 0 -1.867 1.704 1.184
46 H25B H H25B N N N 0 -0.152 1.247 1.314



RZX : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C1 C2 C C doub 1.4 N Y
2 C1 C6 C C sing 1.37 N Y
3 C2 C3 C C sing 1.41 N Y
4 C2 N9 C N sing 1.36 N Y
5 C3 C4 C C doub 1.39 N Y
6 C3 N7 C N sing 1.38 N Y
7 C4 C5 C C sing 1.38 N Y
8 C5 C6 C C doub 1.39 N Y
9 N7 C8 N C sing 1.36 N Y
10 C8 N9 C N doub 1.3 N Y
11 C8 S10 C S sing 1.76 N N
12 S10 C11 S C sing 1.81 N N
13 S10 O18 S O doub 1.42 N N
14 C11 C12 C C sing 1.51 N N
15 C12 N13 C N doub 1.32 N Y
16 C12 C17 C C sing 1.38 N Y
17 N13 C14 N C sing 1.32 N Y
18 C14 C15 C C doub 1.38 N Y
19 C15 C16 C C sing 1.39 N Y
20 C16 C17 C C doub 1.39 N Y
21 C16 O19 C O sing 1.36 N N
22 C17 C25 C C sing 1.51 N N
23 O19 C20 O C sing 1.43 N N
24 C20 C21 C C sing 1.53 N N
25 C21 C22 C C sing 1.53 N N
26 C22 O23 C O sing 1.43 N N
27 O23 C24 O C sing 1.43 N N
28 C1 H1 C H sing 1.08 N N
29 C4 H4 C H sing 1.08 N N
30 C5 H5 C H sing 1.08 N N
31 C6 H6 C H sing 1.08 N N
32 N7 HN7 N H sing 0.97 N N
33 C11 H11 C H sing 1.09 N N
34 C11 H11A C H sing 1.09 N N
35 C14 H14 C H sing 1.08 N N
36 C15 H15 C H sing 1.08 N N
37 C20 H20 C H sing 1.09 N N
38 C20 H20A C H sing 1.09 N N
39 C21 H21 C H sing 1.09 N N
40 C21 H21A C H sing 1.09 N N
41 C22 H22 C H sing 1.09 N N
42 C22 H22A C H sing 1.09 N N
43 C24 H24 C H sing 1.09 N N
44 C24 H24A C H sing 1.09 N N
45 C24 H24B C H sing 1.09 N N
46 C25 H25 C H sing 1.09 N N
47 C25 H25A C H sing 1.09 N N
48 C25 H25B C H sing 1.09 N N



RZX : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
RZX 3pgl Open in New Window Bound ligand 1 1