Chemical Components in the PDB

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IMW : Summary

Code

IMW

One-letter code

X

Molecule name

2-methyl-5-(1-methylethyl)cyclohexa-2,5-diene-1,4-dione

Synonyms

Thymoquinone
2-isopropyl-5-methylbenzo-1,4-quinone

Systematic names

ProgramVersionName
ACDLabs 12.01 2-methyl-5-(propan-2-yl)cyclohexa-2,5-diene-1,4-dione
OpenEye OEToolkits 1.7.0 2-methyl-5-propan-2-yl-cyclohexa-2,5-diene-1,4-dione

Formula

C10 H12 O2

Formal charge

0

Molecular weight

164.201 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1C=C(C(=O)C=C1C(C)C)C
SMILES CACTVS 3.370 CC(C)C1=CC(=O)C(=CC1=O)C
SMILES OpenEye OEToolkits 1.7.0 CC1=CC(=O)C(=CC1=O)C(C)C
Canonical SMILES CACTVS 3.370 CC(C)C1=CC(=O)C(=CC1=O)C
Canonical SMILES OpenEye OEToolkits 1.7.0 CC1=CC(=O)C(=CC1=O)C(C)C

IUPAC InChI

InChI=1S/C10H12O2/c1-6(2)8-5-9(11)7(3)4-10(8)12/h4-6H,1-3H3

IUPAC InChI key

KEQHJBNSCLWCAE-UHFFFAOYSA-N
IMW

wwPDB Information

Atom count

24 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-05-06

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



IMW : Atoms of Molecule

Total Number of Atoms: 24
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 CAA C CAA N N N 0 1.977 -0.51 -0.002
2 CAB C CAB N N N 0 1.009 -1.437 -0.002
3 CAC C CAC N N N 0 -0.409 -1.024 -0.001
4 CAD C CAD N N N 0 -0.761 0.41 0.0
5 CAE C CAE N N N 0 0.206 1.337 0.001
6 CAF C CAF N N N 0 1.625 0.925 -0.001
7 CAG C CAG N N N 0 3.424 -0.93 0.003
8 CAH C CAH N N N 0 -2.208 0.831 0.001
9 CAI C CAI N N N 0 -2.9 0.282 -1.249
10 OAJ O OAJ N N N 0 2.501 1.765 -0.001
11 OAK O OAK N N N 0 -1.286 -1.865 -0.001
12 CAL C CAL N N N 0 -2.899 0.28 1.25
13 HAB H HAB N N N 0 1.266 -2.486 -0.002
14 HAE H HAE N N N 0 -0.051 2.386 0.001
15 HAG H HAG N N N 0 3.775 -1.035 -1.024
16 HAGA H HAGA N N N 0 4.02 -0.176 0.516
17 HAGB H HAGB N N N 0 3.523 -1.885 0.52
18 HAH H HAH N N N 0 -2.27 1.919 0.002
19 HAI H HAI N N N 0 -3.946 0.586 -1.248
20 HAIA H HAIA N N N 0 -2.407 0.674 -2.138
21 HAIB H HAIB N N N 0 -2.838 -0.807 -1.249
22 HAL H HAL N N N 0 -2.407 0.671 2.14
23 HALA H HALA N N N 0 -3.946 0.584 1.25
24 HALB H HALB N N N 0 -2.837 -0.808 1.249



IMW : Chemical Bonds

Total Number of Bonds: 24
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAA CAB C C doub 1.34 N N
2 CAA CAF C C sing 1.48 N N
3 CAA CAG C C sing 1.51 N N
4 CAB CAC C C sing 1.48 N N
5 CAC CAD C C sing 1.48 N N
6 CAC OAK C O doub 1.22 N N
7 CAD CAE C C doub 1.34 N N
8 CAD CAH C C sing 1.51 N N
9 CAE CAF C C sing 1.48 N N
10 CAF OAJ C O doub 1.21 N N
11 CAH CAI C C sing 1.53 N N
12 CAH CAL C C sing 1.53 N N
13 CAB HAB C H sing 1.08 N N
14 CAE HAE C H sing 1.08 N N
15 CAG HAG C H sing 1.09 N N
16 CAG HAGA C H sing 1.09 N N
17 CAG HAGB C H sing 1.09 N N
18 CAH HAH C H sing 1.09 N N
19 CAI HAI C H sing 1.09 N N
20 CAI HAIA C H sing 1.09 N N
21 CAI HAIB C H sing 1.09 N N
22 CAL HAL C H sing 1.09 N N
23 CAL HALA C H sing 1.09 N N
24 CAL HALB C H sing 1.09 N N



IMW : Used in PDB Entries

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