Chemical Components in the PDB

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UVJ : Summary

Code

UVJ

One-letter code

X

Molecule name

3-(2-methyl-1H-benzimidazol-1-yl)propanamide

Systematic names

ProgramVersionName
ACDLabs 12.01 3-(2-methyl-1H-benzimidazol-1-yl)propanamide
OpenEye OEToolkits 2.0.7 3-(2-methylbenzimidazol-1-yl)propanamide

Formula

C11 H13 N3 O

Formal charge

0

Molecular weight

203.24 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 n2(c1ccccc1nc2C)CCC(N)=O
SMILES CACTVS 3.385 Cc1nc2ccccc2n1CCC(N)=O
SMILES OpenEye OEToolkits 2.0.7 Cc1nc2ccccc2n1CCC(=O)N
Canonical SMILES CACTVS 3.385 Cc1nc2ccccc2n1CCC(N)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 Cc1nc2ccccc2n1CCC(=O)N

IUPAC InChI

InChI=1S/C11H13N3O/c1-8-13-9-4-2-3-5-10(9)14(8)7-6-11(12)15/h2-5H,6-7H2,1H3,(H2,12,15)

IUPAC InChI key

HZTUIHZIQKFSIL-UHFFFAOYSA-N
UVJ

wwPDB Information

Atom count

28 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-06-02

Last modified at

2020-06-12

Status

Released

Obsoleted

Not Assigned



UVJ : Atoms of Molecule

Total Number of Atoms: 28
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N1 N N1 N Y N 0 -0.118 -0.543 -0.334
2 C4 C C1 N Y N 0 -3.707 1.405 0.223
3 C5 C C2 N Y N 0 -2.644 2.21 -0.158
4 C6 C C3 N Y N 0 -1.391 1.666 -0.354
5 C7 C C4 N Y N 0 -1.203 0.3 -0.199
6 C8 C C5 N N N 0 1.242 -0.153 -0.715
7 C10 C C6 N N N 0 3.445 0.587 0.15
8 N N N2 N Y N 0 -1.81 -1.786 0.261
9 C C C7 N N N 0 0.324 -3.033 -0.06
10 O O O1 N N N 0 3.767 0.6 -1.02
11 C1 C C8 N Y N 0 -0.544 -1.801 -0.042
12 C2 C C9 N Y N 0 -2.284 -0.516 0.178
13 C3 C C10 N Y N 0 -3.538 0.06 0.392
14 H2 H H2 N N N 0 -2.797 3.269 -0.304
15 C9 C C11 N N N 0 2.046 0.186 0.542
16 N2 N N3 N N N 0 4.338 0.93 1.098
17 H1 H H1 N N N 0 -4.683 1.844 0.373
18 H3 H H3 N N N 0 -0.567 2.297 -0.651
19 H4 H H4 N N N 0 1.722 -0.978 -1.242
20 H5 H H5 N N N 0 1.2 0.72 -1.366
21 H6 H H6 N N N 0 0.294 -3.483 -1.052
22 H7 H H7 N N N 0 1.35 -2.757 0.183
23 H8 H H8 N N N 0 -0.045 -3.748 0.675
24 H9 H H9 N N N 0 -4.373 -0.557 0.689
25 H10 H H10 N N N 0 1.566 1.01 1.069
26 H11 H H11 N N N 0 2.087 -0.687 1.193
27 H12 H H12 N N N 0 5.239 1.188 0.846
28 H13 H H13 N N N 0 4.081 0.92 2.034



UVJ : Chemical Bonds

Total Number of Bonds: 29
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C C1 C C sing 1.51 N N
2 N C1 N C doub 1.3 N Y
3 N C2 N C sing 1.36 N Y
4 C1 N1 C N sing 1.36 N Y
5 C2 C3 C C doub 1.4 N Y
6 C2 C7 C C sing 1.41 N Y
7 C3 C4 C C sing 1.37 N Y
8 O C10 O C doub 1.21 N N
9 N1 C7 N C sing 1.38 N Y
10 N1 C8 N C sing 1.47 N N
11 C9 C10 C C sing 1.51 N N
12 C9 C8 C C sing 1.53 N N
13 C7 C6 C C doub 1.39 N Y
14 C4 C5 C C doub 1.39 N Y
15 C10 N2 C N sing 1.35 N N
16 C6 C5 C C sing 1.38 N Y
17 C4 H1 C H sing 1.08 N N
18 C5 H2 C H sing 1.08 N N
19 C6 H3 C H sing 1.08 N N
20 C8 H4 C H sing 1.09 N N
21 C8 H5 C H sing 1.09 N N
22 C H6 C H sing 1.09 N N
23 C H7 C H sing 1.09 N N
24 C H8 C H sing 1.09 N N
25 C3 H9 C H sing 1.08 N N
26 C9 H10 C H sing 1.09 N N
27 C9 H11 C H sing 1.09 N N
28 N2 H12 N H sing 0.97 N N
29 N2 H13 N H sing 0.97 N N



UVJ : Used in PDB Entries

Total Number of PDB Entries: 3
Ligand Code PDB Entry ID Type Total Distinct
UVJ 5rk8 Open in New Window Bound ligand 1 1
UVJ 5rlt Open in New Window Bound ligand 1 1
UVJ 7gp6 Open in New Window Bound ligand 1 1