Chemical Components in the PDB

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OEN : Summary

Code

OEN

One-letter code

X

Molecule name

Biapenem Imine hydrolysis product

Systematic names

ProgramVersionName
OpenEye OEToolkits 2.0.7 (4~{R})-5-[(2~{S},3~{R})-1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-3-[[(6~{S})-6,7-dihydro-5~{H}-pyrazolo[1,2-a][1,2,4]triazol-4-ium-6-yl]sulfanyl]-4-methyl-3,4-dihydro-2~{H}-pyrrole-2-carboxylic acid

Formula

C15 H21 N4 O5 S

Formal charge

1

Molecular weight

369.416 Da

SMILES

TypeProgramVersionDescriptor
SMILES CACTVS 3.385 C[CH](O)[CH](C(O)=O)C1=N[CH]([CH](S[CH]2Cn3cnc[n+]3C2)[CH]1C)C(O)=O
SMILES OpenEye OEToolkits 2.0.7 CC1C(C(N=C1C(C(C)O)C(=O)O)C(=O)O)SC2Cn3cnc[n+]3C2
Canonical SMILES CACTVS 3.385 C[C@@H](O)[C@@H](C(O)=O)C1=N[C@@H]([C@@H](S[C@H]2Cn3cnc[n+]3C2)[C@@H]1C)C(O)=O
Canonical SMILES OpenEye OEToolkits 2.0.7 C[C@H]1C(C(N=C1[C@@H]([C@@H](C)O)C(=O)O)C(=O)O)S[C@H]2Cn3cnc[n+]3C2

IUPAC InChI

InChI=1S/C15H20N4O5S/c1-7-11(10(8(2)20)14(21)22)17-12(15(23)24)13(7)25-9-3-18-5-16-6-19(18)4-9/h5-10,12-13,20H,3-4H2,1-2H3,(H-,21,22,23,24)/p+1/t7-,8-,10-,12+,13+/m1/s1

IUPAC InChI key

FWQUIKBOZBJCAG-PAMYDDKSSA-O
OEN

wwPDB Information

Atom count

46 (25 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2020-03-02

Last modified at

2021-03-26

Status

Released

Obsoleted

Not Assigned



OEN : Atoms of Molecule

Total Number of Atoms: 46
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 N N N1 N Y N 1 4.93 -0.868 0.323
2 C C C1 N N N 0 -0.951 2.934 0.199
3 O O O1 N N N 0 0.041 3.708 0.667
4 C1 C C2 R N N 0 -1.123 1.531 0.722
5 C10 C C3 N N N 0 -2.293 -0.22 -0.155
6 C11 C C4 S N N 0 -3.441 -1.046 -0.677
7 C12 C C5 R N N 0 -3.694 -2.223 0.267
8 C13 C C6 N N N 0 -2.505 -3.184 0.214
9 C14 C C7 N N N 0 -4.679 -0.191 -0.758
10 C2 C C8 S N N 0 -0.045 0.598 0.121
11 C3 C C9 S N N 0 2.565 -0.509 0.275
12 C4 C C10 N N N 0 3.727 -1.024 1.152
13 C5 C C11 N Y N 0 6.188 -1.253 0.196
14 C6 C C12 N Y N 0 5.786 0.098 -1.44
15 C7 C C13 N N N 0 3.281 0.485 -0.668
16 C8 C C14 R N N 0 -0.862 -0.703 -0.071
17 C9 C C15 N N N 0 -0.456 -1.407 -1.367
18 N1 N N2 N Y N 0 6.699 -0.666 -0.87
19 N2 N N3 N Y N 0 4.669 0.009 -0.739
20 N3 N N4 N N N 0 -2.404 0.974 0.273
21 O1 O O2 N N N 0 -3.855 -1.737 1.601
22 O2 O O3 N N N 0 -4.616 0.989 -0.507
23 O3 O O4 N N N 0 -5.852 -0.741 -1.11
24 O4 O O5 N N N 0 -1.705 3.362 -0.642
25 S S S1 N N N 0 1.324 0.345 1.285
26 H1 H H1 N N N 0 0.158 4.572 0.249
27 H2 H H2 N N N 0 -1.066 1.524 1.81
28 H4 H H4 N N N 0 -3.194 -1.423 -1.67
29 H5 H H5 N N N 0 -4.599 -2.747 -0.04
30 H6 H H6 N N N 0 -2.73 -4.073 0.805
31 H7 H H7 N N N 0 -2.317 -3.473 -0.82
32 H8 H H8 N N N 0 -1.621 -2.692 0.621
33 H9 H H9 N N N 0 0.318 0.98 -0.833
34 H10 H H10 N N N 0 2.113 -1.325 -0.288
35 H11 H H11 N N N 0 3.574 -2.074 1.404
36 H12 H H12 N N N 0 3.811 -0.425 2.059
37 H13 H H13 N N N 0 6.71 -1.933 0.854
38 H14 H H14 N N N 0 5.929 0.695 -2.329
39 H15 H H15 N N N 0 2.826 0.463 -1.658
40 H16 H H16 N N N 0 3.241 1.494 -0.256
41 H17 H H17 N N N 0 -0.732 -1.367 0.784
42 H18 H H18 N N N 0 -0.484 -0.694 -2.191
43 H19 H H19 N N N 0 0.554 -1.803 -1.263
44 H20 H H20 N N N 0 -1.148 -2.224 -1.569
45 H23 H H23 N N N 0 -4.019 -2.43 2.255
46 H24 H H24 N N N 0 -6.619 -0.152 -1.148



OEN : Chemical Bonds

Total Number of Bonds: 48
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O1 C12 O C sing 1.43 N N
2 C12 C13 C C sing 1.53 N N
3 C12 C11 C C sing 1.53 N N
4 O2 C14 O C doub 1.21 N N
5 C14 C11 C C sing 1.51 N N
6 C14 O3 C O sing 1.34 N N
7 C11 C10 C C sing 1.51 N N
8 C10 N3 C N doub 1.27 N N
9 C10 C8 C C sing 1.51 N N
10 N3 C1 N C sing 1.47 N N
11 C9 C8 C C sing 1.53 N N
12 C8 C2 C C sing 1.55 N N
13 C1 C2 C C sing 1.55 N N
14 C1 C C C sing 1.51 N N
15 O4 C O C doub 1.21 N N
16 C2 S C S sing 1.81 N N
17 C O C O sing 1.34 N N
18 S C3 S C sing 1.81 N N
19 C3 C4 C C sing 1.54 N N
20 C3 C7 C C sing 1.55 N N
21 C4 N C N sing 1.47 N N
22 C7 N2 C N sing 1.47 N N
23 N N2 N N sing 1.4 N Y
24 N C5 N C doub 1.32 N Y
25 N2 C6 N C sing 1.32 N Y
26 C5 N1 C N sing 1.32 N Y
27 C6 N1 C N doub 1.32 N Y
28 O H1 O H sing 0.97 N N
29 C1 H2 C H sing 1.09 N N
30 C11 H4 C H sing 1.09 N N
31 C12 H5 C H sing 1.09 N N
32 C13 H6 C H sing 1.09 N N
33 C13 H7 C H sing 1.09 N N
34 C13 H8 C H sing 1.09 N N
35 C2 H9 C H sing 1.09 N N
36 C3 H10 C H sing 1.09 N N
37 C4 H11 C H sing 1.09 N N
38 C4 H12 C H sing 1.09 N N
39 C5 H13 C H sing 1.08 N N
40 C6 H14 C H sing 1.08 N N
41 C7 H15 C H sing 1.09 N N
42 C7 H16 C H sing 1.09 N N
43 C8 H17 C H sing 1.09 N N
44 C9 H18 C H sing 1.09 N N
45 C9 H19 C H sing 1.09 N N
46 C9 H20 C H sing 1.09 N N
47 O1 H23 O H sing 0.97 N N
48 O3 H24 O H sing 0.97 N N



OEN : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
OEN 6y6j Open in New Window Bound ligand 1 1