Chemical Components in the PDB

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4IZ : Summary

Code

4IZ

One-letter code

X

Molecule name

beta-D-galactopyranosyl 1-seleno-beta-D-galactopyranoside

Systematic names

ProgramVersionName
ACDLabs 12.01 beta-D-galactopyranosyl 1-seleno-beta-D-galactopyranoside
OpenEye OEToolkits 2.0.7 (2~{R},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]selanyl-oxane-3,4,5-triol

Formula

C12 H22 O10 Se

Formal charge

0

Molecular weight

405.257 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 12.01 OC1C(OC(CO)C(O)C1O)[Se]C1OC(CO)C(O)C(O)C1O
SMILES CACTVS 3.385 OC[CH]1O[CH]([Se][CH]2O[CH](CO)[CH](O)[CH](O)[CH]2O)[CH](O)[CH](O)[CH]1O
SMILES OpenEye OEToolkits 2.0.7 C(C1C(C(C(C(O1)[Se]C2C(C(C(C(O2)CO)O)O)O)O)O)O)O
Canonical SMILES CACTVS 3.385 OC[C@H]1O[C@@H]([Se][C@@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2O)[C@H](O)[C@@H](O)[C@H]1O
Canonical SMILES OpenEye OEToolkits 2.0.7 C([C@@H]1[C@@H]([C@@H]([C@H]([C@@H](O1)[Se][C@H]2[C@@H]([C@H]([C@H]([C@H](O2)CO)O)O)O)O)O)O)O

IUPAC InChI

InChI=1S/C12H22O10Se/c13-1-3-5(15)7(17)9(19)11(21-3)23-12-10(20)8(18)6(16)4(2-14)22-12/h3-20H,1-2H2/t3-,4-,5+,6+,7+,8+,9-,10-,11+,12+/m1/s1

IUPAC InChI key

XCXHDIQHVBWOAM-ZFDCCPEWSA-N
4IZ

wwPDB Information

Atom count

45 (23 without Hydrogen)

Polymer type

Bound ligand

Type description

non-polymer

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2021-07-12

Last modified at

2022-07-08

Status

Released

Obsoleted

Not Assigned



4IZ : Atoms of Molecule

Total Number of Atoms: 45
Record Atom Name Symbol PDB Name Stereochemistry Is Aromatic Is Leaving Atom Charge X-Coordinate Y-Coordinate Z-Coordinate
1 C4 C C1 R N N 0 4.062 -0.789 0.201
2 C5 C C2 R N N 0 2.749 -1.508 0.522
3 C6 C C3 N N N 0 2.923 -2.345 1.791
4 C3 C C4 S N N 0 3.864 0.093 -1.035
5 O2 O O1 N N N 0 2.475 1.852 -1.944
6 C2 C C5 R N N 0 2.716 1.073 -0.771
7 O3 O O2 N N N 0 5.064 0.823 -1.298
8 O4 O O3 N N N 0 4.445 0.024 1.312
9 O6 O O4 N N N 0 1.736 -3.106 2.026
10 O5 O O5 N N N 0 1.716 -0.542 0.727
11 C1 C C6 S N N 0 1.454 0.283 -0.413
12 SE1 SE SE1 N N N 0 -0.001 1.529 0.001
13 CAN C C7 S N N 0 -1.455 0.282 0.414
14 OAO O O6 N N N 0 -1.716 -0.539 -0.726
15 CAP C C8 R N N 0 -2.748 -1.507 -0.524
16 CAV C C9 N N N 0 -2.92 -2.343 -1.794
17 OAW O O7 N N N 0 -1.732 -3.101 -2.03
18 CAQ C C10 R N N 0 -4.062 -0.79 -0.203
19 OAU O O8 N N N 0 -4.446 0.024 -1.312
20 CAR C C11 S N N 0 -3.865 0.09 1.035
21 OAT O O9 N N N 0 -5.065 0.819 1.299
22 CAM C C12 R N N 0 -2.717 1.071 0.773
23 OAS O O10 N N N 0 -2.476 1.849 1.947
24 H1 H H1 N N N 0 4.841 -1.525 0.003
25 H2 H H2 N N N 0 2.478 -2.159 -0.309
26 H3 H H3 N N N 0 3.769 -3.021 1.667
27 H4 H H4 N N N 0 3.105 -1.686 2.64
28 H5 H H5 N N N 0 3.622 -0.532 -1.894
29 H6 H H6 N N N 0 1.759 2.495 -1.849
30 H7 H H7 N N N 0 2.982 1.731 0.055
31 H8 H H8 N N N 0 5.008 1.409 -2.066
32 H9 H H9 N N N 0 5.27 0.511 1.177
33 H10 H H10 N N N 0 1.775 -3.662 2.816
34 H11 H H11 N N N 0 1.167 -0.344 -1.257
35 H12 H H12 N N N 0 -1.167 -0.346 1.256
36 H13 H H13 N N N 0 -2.477 -2.159 0.306
37 H14 H H14 N N N 0 -3.765 -3.02 -1.671
38 H15 H H15 N N N 0 -3.104 -1.682 -2.641
39 H16 H H16 N N N 0 -1.77 -3.655 -2.821
40 H17 H H17 N N N 0 -4.84 -1.528 -0.005
41 H18 H H18 N N N 0 -5.272 0.508 -1.178
42 H19 H H19 N N N 0 -3.621 -0.536 1.893
43 H20 H H20 N N N 0 -5.011 1.399 2.071
44 H21 H H21 N N N 0 -2.983 1.729 -0.054
45 H22 H H22 N N N 0 -1.757 2.489 1.853



4IZ : Chemical Bonds

Total Number of Bonds: 46
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 OAW CAV O C sing 1.43 N N
2 CAV CAP C C sing 1.53 N N
3 CAP OAO C O sing 1.43 N N
4 CAP CAQ C C sing 1.53 N N
5 O2 C2 O C sing 1.43 N N
6 OAO CAN O C sing 1.43 N N
7 C3 O3 C O sing 1.43 N N
8 C3 C2 C C sing 1.53 N N
9 C3 C4 C C sing 1.53 N N
10 C1 C2 C C sing 1.53 N N
11 C1 SE1 C SE sing 1.96 N N
12 C1 O5 C O sing 1.43 N N
13 CAQ OAU C O sing 1.43 N N
14 CAQ CAR C C sing 1.53 N N
15 C5 C4 C C sing 1.53 N N
16 C5 O5 C O sing 1.43 N N
17 C5 C6 C C sing 1.53 N N
18 CAN SE1 C SE sing 1.96 N N
19 CAN CAM C C sing 1.53 N N
20 C4 O4 C O sing 1.43 N N
21 O6 C6 O C sing 1.43 N N
22 CAR CAM C C sing 1.53 N N
23 CAR OAT C O sing 1.43 N N
24 CAM OAS C O sing 1.43 N N
25 C4 H1 C H sing 1.09 N N
26 C5 H2 C H sing 1.09 N N
27 C6 H3 C H sing 1.09 N N
28 C6 H4 C H sing 1.09 N N
29 C3 H5 C H sing 1.09 N N
30 O2 H6 O H sing 0.97 N N
31 C2 H7 C H sing 1.09 N N
32 O3 H8 O H sing 0.97 N N
33 O4 H9 O H sing 0.97 N N
34 O6 H10 O H sing 0.97 N N
35 C1 H11 C H sing 1.09 N N
36 CAN H12 C H sing 1.09 N N
37 CAP H13 C H sing 1.09 N N
38 CAV H14 C H sing 1.09 N N
39 CAV H15 C H sing 1.09 N N
40 OAW H16 O H sing 0.97 N N
41 CAQ H17 C H sing 1.09 N N
42 OAU H18 O H sing 0.97 N N
43 CAR H19 C H sing 1.09 N N
44 OAT H20 O H sing 0.97 N N
45 CAM H21 C H sing 1.09 N N
46 OAS H22 O H sing 0.97 N N



4IZ : Used in PDB Entries

Total Number of PDB Entries: 1
Ligand Code PDB Entry ID Type Total Distinct
4IZ 7rdp Open in New Window Bound ligand 1 1