Chemical Components in the PDB

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J01 : Summary

Code

J01

One-letter code

X

Molecule name

(2R,3Z,5R)-3-(2-HYDROXYETHYLIDENE)-7-OXO-4-OXA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID

Synonyms

CLAVULANIC ACID

Systematic names

ProgramVersionName
ACDLabs 10.04 (2R,3Z,5R)-3-(2-hydroxyethylidene)-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid
OpenEye OEToolkits 1.5.0 (2R,3Z,5R)-3-(2-hydroxyethylidene)-7-oxo-4-oxa-1-azabicyclo[3.2.0]heptane-2-carboxylic acid

Formula

C8 H9 N O5

Formal charge

0

Molecular weight

199.161 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 O=C2N1C(C(/OC1C2)=C/CO)C(=O)O
SMILES CACTVS 3.341 OCC=C1O[CH]2CC(=O)N2[CH]1C(O)=O
SMILES OpenEye OEToolkits 1.5.0 C1C2N(C1=O)C(C(=CCO)O2)C(=O)O
Canonical SMILES CACTVS 3.341 OC\C=C1/O[C@@H]2CC(=O)N2[C@H]1C(O)=O
Canonical SMILES OpenEye OEToolkits 1.5.0 C1[C@@H]2N(C1=O)[C@H](/C(=C/CO)/O2)C(=O)O

IUPAC InChI

InChI=1S/C8H9NO5/c10-2-1-4-7(8(12)13)9-5(11)3-6(9)14-4/h1,6-7,10H,2-3H2,(H,12,13)/b4-1-/t6-,7-/m1/s1

IUPAC InChI key

HZZVJAQRINQKSD-PBFISZAISA-N
J01

wwPDB Information

Atom count

23 (14 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-11-29

Last modified at

2011-06-04

Status

Released

Obsoleted

Not Assigned



J01 : Atoms of Molecule

Total Number of Atoms: 23
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 O2 O O2 N N N 0 4.193 3.714 -1.975
2 C5 C C5 N N N 0 3.433 3.701 -1.034
3 C4 C C4 N N N 0 2.173 4.483 -0.62
4 C3 C C3 R N N 0 2.02 3.421 0.483
5 N1 N N1 N N N 0 3.297 2.86 0.034
6 O1 O O1 N N N 0 0.993 2.407 0.357
7 C1 C C1 N N N 0 1.714 1.23 0.08
8 C2 C C2 R N N 0 3.206 1.427 -0.059
9 C8 C C8 N N N 0 3.916 0.85 1.122
10 O5 O O5 N N N 0 3.659 1.106 2.289
11 O4 O O4 N N N 0 4.893 -0.0010 0.724
12 C6 C C6 N N N 0 1.079 0.066 -0.092
13 C7 C C7 N N N 0 -0.397 -0.107 0.05
14 O3 O O3 N N N 0 -0.923 -0.574 -1.184
15 H4C1 H 1H4C N N N 0 2.374 5.498 -0.27
16 H4C2 H 2H4C N N N 0 1.387 4.49 -1.38
17 H3 H H3 N N N 0 2.073 3.815 1.504
18 H2 H H2 N N N 0 3.604 1.057 -1.007
19 H6 H H6 N N N 0 1.664 -0.815 -0.343
20 H4 H H4 N N N 0 5.373 -0.389 1.486
21 H7C1 H 1H7C N N N 0 -0.9 0.829 0.312
22 H7C2 H 2H7C N N N 0 -0.61 -0.851 0.824
23 HA H HA N N N 0 -0.183 -0.968 -1.674



J01 : 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 O2 C5 O C doub 1.21 N N
2 C5 C4 C C sing 1.54 N N
3 C5 N1 C N sing 1.37 N N
4 C4 C3 C C sing 1.54 N N
5 C4 H4C1 C H sing 1.09 N N
6 C4 H4C2 C H sing 1.09 N N
7 C3 N1 C N sing 1.47 N N
8 C3 O1 C O sing 1.45 N N
9 C3 H3 C H sing 1.1 N N
10 N1 C2 N C sing 1.44 N N
11 O1 C1 O C sing 1.41 N N
12 C1 C2 C C sing 1.51 N N
13 C1 C6 C C doub 1.34 Z N
14 C2 C8 C C sing 1.49 N N
15 C2 H2 C H sing 1.09 N N
16 C8 O5 C O doub 1.22 N N
17 C8 O4 C O sing 1.36 N N
18 O4 H4 O H sing 0.98 N N
19 C6 C7 C C sing 1.49 N N
20 C6 H6 C H sing 1.09 N N
21 C7 O3 C O sing 1.42 N N
22 C7 H7C1 C H sing 1.09 N N
23 C7 H7C2 C H sing 1.09 N N
24 O3 HA O H sing 0.97 N N



J01 : Used in PDB Entries

Total Number of PDB Entries: 6
Ligand Code PDB Entry ID Type Total Distinct
J01 2jap Open in New Window Bound ligand 4 1
J01 2xf3 Open in New Window Bound ligand 4 1
J01 2xfs Open in New Window Bound ligand 4 1
J01 2xh9 Open in New Window Bound ligand 4 1
J01 6nvu Open in New Window Bound ligand 2 1
J01 6pq8 Open in New Window Bound ligand 1 1