Chemical Components in the PDB

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RVF : Summary

Code

RVF

One-letter code

X

Molecule name

3-{[(2-hydroxy-1H-benzimidazole-5-carbonyl)amino]methyl}-1H-indole-2-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 3-{[(2-hydroxy-1H-benzimidazole-5-carbonyl)amino]methyl}-1H-indole-2-carboxylic acid
OpenEye OEToolkits 2.0.7 3-[[(2-oxidanyl-1~{H}-benzimidazol-5-yl)carbonylamino]methyl]-1~{H}-indole-2-carboxylic acid

Formula

C18 H14 N4 O4

Formal charge

0

Molecular weight

350.328 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)c1[NH]c2ccccc2c1CNC(=O)c1cc2nc(O)[NH]c2cc1
SMILES CACTVS 3.385 OC(=O)c1[nH]c2ccccc2c1CNC(=O)c3ccc4[nH]c(O)nc4c3
SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)c(c([nH]2)C(=O)O)CNC(=O)c3ccc4c(c3)nc([nH]4)O
Canonical SMILES CACTVS 3.385 OC(=O)c1[nH]c2ccccc2c1CNC(=O)c3ccc4[nH]c(O)nc4c3
Canonical SMILES OpenEye OEToolkits 2.0.7 c1ccc2c(c1)c(c([nH]2)C(=O)O)CNC(=O)c3ccc4c(c3)nc([nH]4)O

IUPAC InChI

InChI=1S/C18H14N4O4/c23-16(9-5-6-13-14(7-9)22-18(26)21-13)19-8-11-10-3-1-2-4-12(10)20-15(11)17(24)25/h1-7,20H,8H2,(H,19,23)(H,24,25)(H2,21,22,26)

IUPAC InChI key

XGVGMKBKRWQGTN-UHFFFAOYSA-N
RVF

wwPDB Information

Atom count

40 (26 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-06-23

Last modified at

2022-07-01

Status

Released

Obsoleted

Not Assigned



RVF : Atoms of Molecule

Total Number of Atoms: 40
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C18 C C1 N Y N 0 -1.963 0.306 0.875
2 C17 C C2 N Y N 0 -2.038 -0.07 -0.472
3 C15 C C3 N N N 0 -0.801 -0.329 -1.235
4 C13 C C4 N N N 0 1.628 -0.458 -1.392
5 C12 C C5 N Y N 0 2.822 -0.248 -0.497
6 C11 C C6 N Y N 0 3.519 0.969 -0.307
7 C10 C C7 N Y N 0 3.359 2.26 -0.826
8 C20 C C8 N Y N 0 -4.345 0.426 0.985
9 C19 C C9 N Y N 0 -3.1 0.547 1.591
10 C02 C C10 N N N 0 3.005 -2.598 0.378
11 C04 C C11 N Y N 0 3.42 -1.193 0.276
12 C06 C C12 N Y N 0 4.559 0.709 0.607
13 C07 C C13 N Y N 0 5.415 1.741 0.981
14 C08 C C14 N Y N 0 5.238 3.001 0.456
15 C09 C C15 N Y N 0 4.211 3.256 -0.444
16 C22 C C16 N Y N 0 -6.469 0.336 0.372
17 C25 C C17 N Y N 0 -4.44 0.044 -0.365
18 C26 C C18 N Y N 0 -3.277 -0.202 -1.093
19 N05 N N1 N Y N 0 4.481 -0.62 0.952
20 N14 N N2 N N N 0 0.4 -0.202 -0.635
21 N21 N N3 N Y N 0 -5.643 0.596 1.426
22 N24 N N4 N Y N 0 -5.763 0.001 -0.676
23 O01 O O1 N N N 0 3.68 -3.444 1.183
24 O03 O O2 N N N 0 2.054 -2.999 -0.264
25 O16 O O3 N N N 0 -0.864 -0.656 -2.404
26 O23 O O4 N N N 0 -7.819 0.396 0.411
27 H181 H H1 N N N 0 -0.999 0.402 1.352
28 H101 H H4 N N N 0 2.564 2.467 -1.528
29 H131 H H2 N N N 0 1.683 0.227 -2.238
30 H132 H H3 N N N 0 1.622 -1.486 -1.756
31 H191 H H5 N N N 0 -3.033 0.832 2.63
32 H071 H H6 N N N 0 6.216 1.554 1.681
33 H081 H H7 N N N 0 5.903 3.801 0.748
34 H091 H H8 N N N 0 4.086 4.25 -0.846
35 H261 H H9 N N N 0 -3.336 -0.491 -2.132
36 H051 H H10 N N N 0 5.073 -1.079 1.568
37 H141 H H11 N N N 0 0.451 0.059 0.298
38 H211 H H12 N N N 0 -5.916 0.854 2.321
39 H2 H H14 N N N 0 3.37 -4.359 1.217
40 H231 H H15 N N N 0 -8.181 1.265 0.187



RVF : Chemical Bonds

Total Number of Bonds: 43
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 C09 C08 C C doub 1.39 N Y
2 C09 C10 C C sing 1.37 N Y
3 C08 C07 C C sing 1.38 N Y
4 C10 C11 C C doub 1.4 N Y
5 C07 C06 C C doub 1.39 N Y
6 C11 C06 C C sing 1.41 N Y
7 C11 C12 C C sing 1.42 N Y
8 C06 N05 C N sing 1.38 N Y
9 C12 C13 C C sing 1.51 N N
10 C12 C04 C C doub 1.36 N Y
11 C13 N14 C N sing 1.47 N N
12 N05 C04 N C sing 1.38 N Y
13 C04 C02 C C sing 1.47 N N
14 O16 C15 O C doub 1.22 N N
15 N14 C15 N C sing 1.35 N N
16 C02 O03 C O doub 1.22 N N
17 C02 O01 C O sing 1.35 N N
18 C15 C17 C C sing 1.48 N N
19 C17 C26 C C doub 1.39 N Y
20 C17 C18 C C sing 1.4 N Y
21 C26 C25 C C sing 1.39 N Y
22 C18 C19 C C doub 1.37 N Y
23 C25 N24 C N sing 1.36 N Y
24 C25 C20 C C doub 1.41 N Y
25 N24 C22 N C doub 1.31 N Y
26 C19 C20 C C sing 1.39 N Y
27 C20 N21 C N sing 1.38 N Y
28 C22 N21 C N sing 1.36 N Y
29 C22 O23 C O sing 1.35 N N
30 C18 H181 C H sing 1.08 N N
31 C13 H131 C H sing 1.09 N N
32 C13 H132 C H sing 1.09 N N
33 C10 H101 C H sing 1.08 N N
34 C19 H191 C H sing 1.08 N N
35 C07 H071 C H sing 1.08 N N
36 C08 H081 C H sing 1.08 N N
37 C09 H091 C H sing 1.08 N N
38 C26 H261 C H sing 1.08 N N
39 N05 H051 N H sing 0.97 N N
40 N14 H141 N H sing 0.97 N N
41 N21 H211 N H sing 0.97 N N
42 O01 H2 O H sing 0.97 N N
43 O23 H231 O H sing 0.97 N N



RVF : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
RVF 5ssr Open in New Window Bound ligand 1 1