Chemical Components in the PDB

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SMX : Summary

Code

SMX

One-letter code

X

Molecule name

(6R,7R)-7-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-3-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid

Synonyms

CEFAMANDOLE, free form

Systematic names

ProgramVersionName
ACDLabs 12.01 (6R,7R)-7-{[(2R)-2-hydroxy-2-phenylacetyl]amino}-3-{[(1-methyl-1H-tetrazol-5-yl)sulfanyl]methyl}-8-oxo-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid
OpenEye OEToolkits 1.7.6 (6R,7R)-3-[(1-methyl-1,2,3,4-tetrazol-5-yl)sulfanylmethyl]-8-oxidanylidene-7-[(2-oxidanyl-2-phenyl-ethanoyl)amino]-5-thia-1-azabicyclo[4.2.0]oct-2-ene-2-carboxylic acid

Formula

C18 H18 N6 O5 S2

Formal charge

0

Molecular weight

462.503 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 O=C(O)C=2N4C(=O)C(NC(=O)C(O)c1ccccc1)C4SCC=2CSc3nnnn3C
SMILES CACTVS 3.370 Cn1nnnc1SCC2=C(N3[CH](SC2)[CH](NC(=O)[CH](O)c4ccccc4)C3=O)C(O)=O
SMILES OpenEye OEToolkits 1.7.6 Cn1c(nnn1)SCC2=C(N3C(C(C3=O)NC(=O)C(c4ccccc4)O)SC2)C(=O)O
Canonical SMILES CACTVS 3.370 Cn1nnnc1SCC2=C(N3[C@H](SC2)[C@H](NC(=O)[C@H](O)c4ccccc4)C3=O)C(O)=O
Canonical SMILES OpenEye OEToolkits 1.7.6 Cn1c(nnn1)SCC2=C(N3[C@@H]([C@@H](C3=O)NC(=O)C(c4ccccc4)O)SC2)C(=O)O

IUPAC InChI

InChI=1S/C18H18N6O5S2/c1-23-18(20-21-22-23)31-8-10-7-30-16-11(15(27)24(16)12(10)17(28)29)19-14(26)13(25)9-5-3-2-4-6-9/h2-6,11,13,16,25H,7-8H2,1H3,(H,19,26)(H,28,29)/t11-,13-,16-/m1/s1

IUPAC InChI key

OLVCFLKTBJRLHI-AXAPSJFSSA-N
SMX

wwPDB Information

Atom count

49 (31 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2010-09-17

Last modified at

2021-03-13

Status

Released

Obsoleted

Not Assigned



SMX : Atoms of Molecule

Total Number of Atoms: 49
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C C C N N N 0 1.067 2.297 -0.512
2 N N N N N N 0 2.981 0.757 -0.112
3 O O O N N N 0 1.09 3.426 -0.069
4 CA C CA R N N 0 2.115 1.397 -1.105
5 CB C CB R N N 0 0.943 0.545 -1.538
6 NBD N NBD N N N 0 0.108 1.392 -0.651
7 NBE N NBE N Y N 0 -6.882 -1.052 -0.264
8 NAN N NAN N Y N 0 -6.873 -1.084 1.901
9 NAO N NAO N Y N 0 -5.67 -0.878 1.5
10 NAP N NAP N Y N 0 -7.668 -1.198 0.892
11 CAA C CAA N N N 0 -7.331 -1.103 -1.658
12 OAB O OAB N N N 0 -2.753 2.773 -0.302
13 OAC O OAC N N N 0 4.657 2.13 -0.589
14 OAE O OAE N N N 0 -1.967 2.428 1.745
15 OAF O OAF N N N 0 6.365 1.259 1.18
16 CAG C CAG N Y N 0 5.905 -3.49 -0.083
17 CAH C CAH N Y N 0 4.878 -3.212 0.799
18 CAI C CAI N Y N 0 6.684 -2.463 -0.583
19 CAJ C CAJ N Y N 0 4.628 -1.907 1.179
20 CAK C CAK N Y N 0 6.433 -1.158 -0.203
21 CAL C CAL N N N 0 -2.938 -0.408 0.497
22 CAM C CAM N N N 0 -0.907 -1.381 -0.68
23 SAR S SAR N N N 0 -4.185 -0.593 -0.802
24 SAS S SAS N N N 0 0.889 -1.139 -0.837
25 CAT C CAT N N N 0 -2.011 2.147 0.428
26 CAU C CAU N N N 0 4.241 1.201 0.07
27 CAV C CAV N N N 0 -1.589 -0.174 -0.132
28 CAX C CAX N N N 0 -1.16 1.079 -0.127
29 CAY C CAY N Y N 0 5.405 -0.88 0.678
30 CAZ C CAZ N Y N 0 -5.621 -0.847 0.186
31 H3 H H3 N N N 0 0.712 0.59 -2.602
32 CBA C CBA R N N 0 5.132 0.543 1.092
33 H1 H H1 N N N 0 2.648 0.014 0.415
34 H2 H H2 N N N 0 2.669 1.845 -1.93
35 H4 H H4 N N N 0 -7.609 -0.101 -1.987
36 H5 H H5 N N N 0 -6.525 -1.482 -2.286
37 H6 H H6 N N N 0 -8.195 -1.763 -1.737
38 H7 H H7 N N N 0 -2.543 3.136 2.063
39 H8 H H8 N N N 0 6.104 -4.51 -0.377
40 H9 H H9 N N N 0 4.269 -4.015 1.189
41 H10 H H10 N N N 0 7.487 -2.68 -1.272
42 H11 H H11 N N N 0 3.824 -1.69 1.868
43 H12 H H12 N N N 0 7.041 -0.355 -0.594
44 H13 H H13 N N N 0 -3.196 0.44 1.13
45 H14 H H14 N N N 0 -2.906 -1.315 1.1
46 H15 H H15 N N N 0 -1.321 -1.606 -1.663
47 H16 H H16 N N N 0 -1.094 -2.226 -0.016
48 H17 H H17 N N N 0 6.86 1.293 0.35
49 H18 H H18 N N N 0 4.637 0.55 2.063



SMX : Chemical Bonds

Total Number of Bonds: 52
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 CAG CAH C C doub 1.38 N Y
2 CAG CAI C C sing 1.38 N Y
3 CAH CAJ C C sing 1.38 N Y
4 CAI CAK C C doub 1.38 N Y
5 CAJ CAY C C doub 1.38 N Y
6 CAK CAY C C sing 1.38 N Y
7 CAY CBA C C sing 1.51 N N
8 CBA OAF C O sing 1.43 N N
9 CBA CAU C C sing 1.51 N N
10 OAC CAU O C doub 1.21 N N
11 CAU N C N sing 1.35 N N
12 N CA N C sing 1.46 N N
13 CA C C C sing 1.5 N N
14 CA CB C C sing 1.51 N N
15 O C O C doub 1.21 N N
16 C NBD C N sing 1.33 N N
17 CB SAS C S sing 1.82 N N
18 CB NBD C N sing 1.48 N N
19 SAS CAM S C sing 1.82 N N
20 NBD CAX N C sing 1.41 N N
21 CAX CAT C C sing 1.47 N N
22 CAX CAV C C doub 1.32 N N
23 CAM CAV C C sing 1.49 N N
24 OAB CAT O C doub 1.21 N N
25 NAN NAO N N sing 1.28 N Y
26 NAN NAP N N doub 1.29 N Y
27 CAT OAE C O sing 1.35 N N
28 CAV CAL C C sing 1.51 N N
29 NAO CAZ N C doub 1.32 N Y
30 NAP NBE N N sing 1.41 N Y
31 CAZ NBE C N sing 1.35 N Y
32 CAZ SAR C S sing 1.76 N N
33 CAL SAR C S sing 1.81 N N
34 NBE CAA N C sing 1.47 N N
35 N H1 N H sing 0.97 N N
36 CA H2 C H sing 1.09 N N
37 CB H3 C H sing 1.09 N N
38 CAA H4 C H sing 1.09 N N
39 CAA H5 C H sing 1.09 N N
40 CAA H6 C H sing 1.09 N N
41 OAE H7 O H sing 0.97 N N
42 CAG H8 C H sing 1.08 N N
43 CAH H9 C H sing 1.08 N N
44 CAI H10 C H sing 1.08 N N
45 CAJ H11 C H sing 1.08 N N
46 CAK H12 C H sing 1.08 N N
47 CAL H13 C H sing 1.09 N N
48 CAL H14 C H sing 1.09 N N
49 CAM H15 C H sing 1.09 N N
50 CAM H16 C H sing 1.09 N N
51 OAF H17 O H sing 0.97 N N
52 CBA H18 C H sing 1.09 N N



SMX : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
SMX 3ny4 Open in New Window Bound ligand 5 1