Chemical Components in the PDB

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MB3 : Summary

Code

MB3

One-letter code

X

Molecule name

1-methylpyrrolidin-2-one

Systematic names

ProgramVersionName
ACDLabs 12.01 1-methylpyrrolidin-2-one
OpenEye OEToolkits 1.7.0 1-methylpyrrolidin-2-one

Formula

C5 H9 N O

Formal charge

0

Molecular weight

99.131 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C1N(C)CCC1
SMILES CACTVS 3.370 CN1CCCC1=O
SMILES OpenEye OEToolkits 1.7.0 CN1CCCC1=O
Canonical SMILES CACTVS 3.370 CN1CCCC1=O
Canonical SMILES OpenEye OEToolkits 1.7.0 CN1CCCC1=O

IUPAC InChI

InChI=1S/C5H9NO/c1-6-4-2-3-5(6)7/h2-4H2,1H3

IUPAC InChI key

SECXISVLQFMRJM-UHFFFAOYSA-N
MB3

wwPDB Information

Atom count

16 (7 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-03-30

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



MB3 : Atoms of Molecule

Total Number of Atoms: 16
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 1.858 1.108 0.056
2 OAB O OAB N N N 0 1.06 -1.652 0.046
3 CAC C CAC N N N 0 -1.87 0.389 0.225
4 CAD C CAD N N N 0 -1.262 -0.988 -0.127
5 CAE C CAE N N N 0 -0.717 1.348 -0.144
6 CAF C CAF N N N 0 0.232 -0.769 -0.029
7 NAG N NAG N N N 0 0.508 0.547 -0.035
8 HAA H HAA N N N 0 2.115 1.269 1.103
9 HAAA H HAAA N N N 0 2.571 0.415 -0.391
10 HAAB H HAAB N N N 0 1.893 2.059 -0.477
11 HAC H HAC N N N 0 -2.754 0.591 -0.38
12 HACA H HACA N N N 0 -2.105 0.452 1.288
13 HAD H HAD N N N 0 -1.585 -1.742 0.59
14 HADA H HADA N N N 0 -1.54 -1.28 -1.139
15 HAE H HAE N N N 0 -0.84 1.711 -1.165
16 HAEA H HAEA N N N 0 -0.684 2.185 0.552



MB3 : Chemical Bonds

Total Number of Bonds: 16
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAA NAG C N sing 1.46 N N
2 CAA HAA C H sing 1.09 N N
3 CAA HAAA C H sing 1.09 N N
4 CAA HAAB C H sing 1.09 N N
5 CAF OAB C O doub 1.21 N N
6 CAE CAC C C sing 1.54 N N
7 CAC CAD C C sing 1.55 N N
8 CAC HAC C H sing 1.09 N N
9 CAC HACA C H sing 1.09 N N
10 CAF CAD C C sing 1.51 N N
11 CAD HAD C H sing 1.09 N N
12 CAD HADA C H sing 1.09 N N
13 NAG CAE N C sing 1.47 N N
14 CAE HAE C H sing 1.09 N N
15 CAE HAEA C H sing 1.09 N N
16 NAG CAF N C sing 1.34 N N



MB3 : Used in PDB Entries

Total Number of PDB Entries: 11
Ligand Code PDB Entry ID Type Total Distinct
MB3 3mb3 Open in New Window Bound ligand 1 1
MB3 3mb4 Open in New Window Bound ligand 2 1
MB3 3p1d Open in New Window Bound ligand 2 1
MB3 3rcw Open in New Window Bound ligand 1 1
MB3 3uvd Open in New Window Bound ligand 1 1
MB3 4a9f Open in New Window Bound ligand 3 1
MB3 4qss Open in New Window Bound ligand 1 1
MB3 5xdt Open in New Window Bound ligand 2 1
MB3 6rvp Open in New Window Bound ligand 1 1
MB3 6yd5 Open in New Window Bound ligand 1 1
MB3 6yd6 Open in New Window Bound ligand 1 1