Chemical Components in the PDB

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CGB : Summary

Code

CGB

One-letter code

X

Molecule name

CALYSTEGINE B2

Systematic names

ProgramVersionName
ACDLabs 10.04 (1R,2S,3R,4S,5R)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol
OpenEye OEToolkits 1.5.0 (1R,2S,3R,4S,5R)-8-azabicyclo[3.2.1]octane-1,2,3,4-tetrol

Formula

C7 H13 N O4

Formal charge

0

Molecular weight

175.182 Da

SMILES

TypeProgramVersionDescriptor
SMILES ACDLabs 10.04 OC12NC(CC1)C(O)C(O)C2O
SMILES CACTVS 3.341 O[CH]1[CH](O)[CH](O)[C]2(O)CC[CH]1N2
SMILES OpenEye OEToolkits 1.5.0 C1CC2(C(C(C(C1N2)O)O)O)O
Canonical SMILES CACTVS 3.341 O[C@@H]1[C@@H](O)[C@H](O)[C@]2(O)CC[C@H]1N2
Canonical SMILES OpenEye OEToolkits 1.5.0 C1C[C@]2([C@H]([C@@H]([C@H]([C@@H]1N2)O)O)O)O

IUPAC InChI

InChI=1S/C7H13NO4/c9-4-3-1-2-7(12,8-3)6(11)5(4)10/h3-6,8-12H,1-2H2/t3-,4+,5-,6+,7-/m1/s1

IUPAC InChI key

FXFBVZOJVHCEDO-IBISWUOJSA-N
CGB

wwPDB Information

Atom count

25 (12 without Hydrogen)

Polymer type

Bound ligand

Type description

NON-POLYMER

Type code

HETAIN

Is modified

No

Standard parent

Not Assigned

Defined at

2006-01-09

Last modified at

2020-06-17

Status

Released

Obsoleted

Not Assigned



CGB : Atoms of Molecule

Total Number of Atoms: 25
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 -2.741 -0.002 -0.471
2 C2 C C2 R N N 0 -1.357 -0.211 -0.183
3 N1 N N1 N N N 0 -0.746 -1.234 -1.072
4 C8 C C8 N N N 0 -1.132 -0.747 1.249
5 C7 C C7 N N N 0 0.11 -1.656 1.14
6 C6 C C6 R N N 0 0.52 -1.589 -0.377
7 C3 C C3 S N N 0 -0.533 1.078 -0.338
8 O3 O O3 N N N 0 -1.132 2.126 0.426
9 C4 C C4 R N N 0 0.889 0.821 0.169
10 O4 O O4 N N N 0 1.701 1.966 -0.096
11 C5 C C5 S N N 0 1.479 -0.4 -0.543
12 O5 O O5 N N N 0 2.746 -0.723 0.033
13 HO H HO N N N 0 -3.183 -0.853 -0.351
14 H1 H H1 N N N 0 -1.343 -2.047 -1.02
15 H8C1 H 1H8C N N N 0 -0.94 0.077 1.937
16 H8C2 H 2H8C N N N 0 -1.996 -1.323 1.579
17 H7C1 H 1H7C N N N 0 0.912 -1.279 1.774
18 H7C2 H 2H7C N N N 0 -0.144 -2.679 1.416
19 H6 H H6 N N N 0 0.947 -2.527 -0.73
20 H3 H H3 N N N 0 -0.499 1.365 -1.389
21 HA H HA N N N 0 -0.578 2.91 0.306
22 H4 H H4 N N N 0 0.862 0.636 1.243
23 HB H HB N N N 0 2.585 1.765 0.241
24 H5 H H5 N N N 0 1.606 -0.178 -1.603
25 HC H HC N N N 0 3.315 0.05 -0.09



CGB : Chemical Bonds

Total Number of Bonds: 26
Record First Atom Second Atom First Element Second Element Bond Order Type Bond Length Bond Stereochemistry Is Aromatic
1 O2 C2 O C sing 1.43 N N
2 O2 HO O H sing 0.97 N N
3 C2 N1 C N sing 1.49 N N
4 C2 C8 C C sing 1.55 N N
5 C2 C3 C C sing 1.54 N N
6 N1 C6 N C sing 1.49 N N
7 N1 H1 N H sing 1.01 N N
8 C8 C7 C C sing 1.54 N N
9 C8 H8C1 C H sing 1.09 N N
10 C8 H8C2 C H sing 1.09 N N
11 C7 C6 C C sing 1.57 N N
12 C7 H7C1 C H sing 1.09 N N
13 C7 H7C2 C H sing 1.09 N N
14 C6 C5 C C sing 1.54 N N
15 C6 H6 C H sing 1.09 N N
16 C3 O3 C O sing 1.43 N N
17 C3 C4 C C sing 1.53 N N
18 C3 H3 C H sing 1.09 N N
19 O3 HA O H sing 0.97 N N
20 C4 O4 C O sing 1.43 N N
21 C4 C5 C C sing 1.53 N N
22 C4 H4 C H sing 1.09 N N
23 O4 HB O H sing 0.97 N N
24 C5 O5 C O sing 1.43 N N
25 C5 H5 C H sing 1.09 N N
26 O5 HC O H sing 0.97 N N



CGB : Used in PDB Entries

Total Number of PDB Entries: 2
Ligand Code PDB Entry ID Type Total Distinct
CGB 2cbv Open in New Window Bound ligand 2 1
CGB 4iie Open in New Window Bound ligand 2 1