Chemical Components in the PDB

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GID : Summary

Code

GID

One-letter code

X

Molecule name

5-nitro-1H-indole-2-carboxylic acid

Systematic names

ProgramVersionName
ACDLabs 12.01 5-nitro-1H-indole-2-carboxylic acid
OpenEye OEToolkits 2.0.7 5-nitro-1~{H}-indole-2-carboxylic acid

Formula

C9 H6 N2 O4

Formal charge

0

Molecular weight

206.155 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=N(=O)c1cc2cc([NH]c2cc1)C(=O)O
SMILES CACTVS 3.385 OC(=O)c1[nH]c2ccc(cc2c1)[N](=O)=O
SMILES OpenEye OEToolkits 2.0.7 c1cc2c(cc1N(=O)=O)cc([nH]2)C(=O)O
Canonical SMILES CACTVS 3.385 OC(=O)c1[nH]c2ccc(cc2c1)[N](=O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 c1cc2c(cc1N(=O)=O)cc([nH]2)C(=O)O

IUPAC InChI

InChI=1S/C9H6N2O4/c12-9(13)8-4-5-3-6(11(14)15)1-2-7(5)10-8/h1-4,10H,(H,12,13)

IUPAC InChI key

LHFOJSCXLFKDIR-UHFFFAOYSA-N
GID

wwPDB Information

Atom count

21 (15 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2022-01-14

Last modified at

2022-12-16

Status

Released

Obsoleted

Not Assigned



GID : Atoms of Molecule

Total Number of Atoms: 21
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C02 C C1 N Y N 0 -2.301 -0.1 -0.001
2 C03 C C2 N Y N 0 -1.33 -1.052 0.001
3 C04 C C3 N Y N 0 1.248 -0.844 0.001
4 C05 C C4 N Y N 0 2.272 0.057 -0.001
5 C06 C C5 N Y N 0 2.013 1.423 -0.002
6 C13 C C6 N N N 0 -3.747 -0.357 -0.001
7 O14 O O1 N N N 0 -4.615 0.674 0.003
8 O15 O O2 N N N 0 -4.161 -1.501 -0.004
9 C07 C C7 N Y N 0 0.719 1.891 -0.002
10 C08 C C8 N Y N 0 -0.343 0.992 -0.001
11 C09 C C9 N Y N 0 -0.078 -0.392 0.0
12 N10 N N1 N N N 1 3.672 -0.424 0.0
13 O12 O O3 N N N -1 3.905 -1.619 0.002
14 O11 O O4 N N N 0 4.591 0.376 -0.001
15 N01 N N2 N Y N 0 -1.709 1.149 0.003
16 H1 H H1 N N N 0 -1.487 -2.121 0.002
17 H2 H H2 N N N 0 1.459 -1.903 0.002
18 H3 H H3 N N N 0 2.836 2.123 -0.003
19 H4 H H4 N N N 0 -5.557 0.455 0.003
20 H5 H H5 N N N 0 0.528 2.955 -0.003
21 H6 H H6 N N N 0 -2.18 1.997 0.006



GID : Chemical Bonds

Total Number of Bonds: 22
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O11 N10 O N doub 1.22 N N
2 N10 O12 N O sing 1.22 N N
3 N10 C05 N C sing 1.48 N N
4 C04 C05 C C doub 1.36 N Y
5 C04 C09 C C sing 1.4 N Y
6 C05 C06 C C sing 1.39 N Y
7 C09 C03 C C sing 1.42 N Y
8 C09 C08 C C doub 1.41 N Y
9 C03 C02 C C doub 1.36 N Y
10 C06 C07 C C doub 1.38 N Y
11 O15 C13 O C doub 1.22 N N
12 C08 C07 C C sing 1.39 N Y
13 C08 N01 C N sing 1.37 N Y
14 C02 C13 C C sing 1.47 N N
15 C02 N01 C N sing 1.38 N Y
16 C13 O14 C O sing 1.35 N N
17 C03 H1 C H sing 1.08 N N
18 C04 H2 C H sing 1.08 N N
19 C06 H3 C H sing 1.08 N N
20 O14 H4 O H sing 0.97 N N
21 C07 H5 C H sing 1.08 N N
22 N01 H6 N H sing 0.97 N N



GID : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
GID 7tc2 Open in New Window Bound ligand 4 1